Pierrick Roger
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_16 |
| git_last_commit: 4525e08 |
| git_last_commit_date: 2022-11-01 11:25:43 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:04:59 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biodbChebi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 180/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.4.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbChebi |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbChebi_1.4.0.tar.gz |
| StartedAt: 2023-04-10 19:18:32 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:20:54 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 142.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbChebi_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/biodbChebi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 2.148 0.153 6.473
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbChebi.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-04-10 19:19:22.990][biodb::testContext]
biodb.INFO [2023-04-10 19:19:22.992][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:22.993][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-10 19:19:22.994][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:22.995][biodb::testContext]
biodb.INFO [2023-04-10 19:19:23.003][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:23.005][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:23.013][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:23.015][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:19:23.016][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.020][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:19:23.040][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.044][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:19:23.045][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.049][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:19:23.050][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:19:23.051][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:19:23.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.055][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:19:23.056][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:19:23.057][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.061][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:19:23.062][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:19:23.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.066][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:19:23.067][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:19:23.068][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:19:23.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.072][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:19:23.073][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.077][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:19:23.078][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:19:23.079][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:19:23.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.082][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:23.083][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:19:23.084][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:19:23.085][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:19:23.086][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:19:23.088][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:19:23.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.091][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:19:23.092][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:19:23.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.096][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:19:23.097][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:19:23.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.101][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:19:23.102][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:19:23.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.106][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:19:23.107][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:19:23.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.111][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:19:23.112][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:19:23.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.116][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:23.117][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:19:23.123][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:19:23.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.127][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:19:23.128][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:19:23.129][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:19:23.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.136][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:19:23.172][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.190][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:19:23.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:23.194][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.195][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.196][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.197][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.198][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:23.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:23.200][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.201][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:19:23.202][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:23.203][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.204][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.205][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:23.205][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:23.205][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:23.205][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:23.205][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:23.207][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:23.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:23.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.220][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.221][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:23.221][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:23.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.223][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.224][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:19:23.226][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.227][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:23.228][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:23.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.231][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.232][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.233][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.234][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:23.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:23.235][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.236][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:19:23.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:23.238][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.239][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.240][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:23.240][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:23.240][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:23.240][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:23.240][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:23.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:23.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.244][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:23.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.246][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.247][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:23.249][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:23.250][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.251][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.252][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:19:23.253][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.254][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:19:23.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:23.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.259][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.260][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.261][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:23.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:23.263][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.263][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:19:23.264][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:23.265][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.267][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:23.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:23.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.274][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:23.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:23.277][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.278][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.279][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:19:23.281][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.282][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:23.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:23.284][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.288][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:23.289][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:23.290][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.291][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:19:23.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:23.293][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.294][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.294][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:23.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:23.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.302][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:23.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:23.304][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.305][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:23.309][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:23.310][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.383][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:19:23.387][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:19:23.389][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:19:23.390][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:19:23.392][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:23.393][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:23.394][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:23.396][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:23.397][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:19:23.398][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:23.400][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:23.401][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:19:23.402][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:23.404][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:23.405][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:19:23.406][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:23.408][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:19:23.409][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:19:23.410][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:23.412][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:19:23.413][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:19:23.414][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:19:23.416][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:19:23.417][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:19:23.418][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:19:23.420][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:19:23.421][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:19:23.422][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:19:23.424][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:19:23.425][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:19:23.426][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:19:23.427][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:19:23.429][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:19:23.430][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:19:23.431][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:19:23.433][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:19:23.434][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:19:23.435][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:19:23.436][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:19:23.438][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:19:23.439][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:19:23.440][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:19:23.442][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:19:23.443][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:19:23.444][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:19:23.445][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:19:23.447][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:19:23.448][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:19:23.449][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:19:23.451][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:19:23.452][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:19:23.453][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:19:23.455][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:19:23.456][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:19:23.458][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:19:23.459][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:19:23.466][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:19:23.467][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:19:23.469][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:19:23.470][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:19:23.471][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:19:23.472][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:19:23.474][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:19:23.475][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:19:23.476][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:19:23.477][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:19:23.479][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:23.480][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:23.481][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:19:23.482][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:19:23.484][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:19:23.485][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:19:23.486][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:19:23.488][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:19:23.489][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:19:23.490][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:19:23.491][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:19:23.493][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:19:23.494][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:19:23.495][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:19:23.496][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:19:23.498][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:19:23.499][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:19:23.505][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:19:23.506][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:23.509][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:23.510][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.512][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:23.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:23.619][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:23.629][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-10 19:19:23.631][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.632][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.633][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.634][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:23.635][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.636][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.637][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.637][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-10 19:19:23.638][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:19:23.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:23.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.641][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-10 19:19:23.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-10 19:19:23.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-10 19:19:23.644][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:23.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:23.645][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:23.645][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:23.646][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:19:23.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.649][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:23.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:23.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:23.652][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:23.653][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:23.653][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-10 19:19:23.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:23.655][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:23.656][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:23.657][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-10 19:19:23.657][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-10 19:19:23.663][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:23.664][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:23.666][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-10 19:19:23.667][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:23.669][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:23.670][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:23.696][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-10 19:19:23.698][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-10 19:19:23.702][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-10 19:19:23.707][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-10 19:19:23.712][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:23.713][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:23.715][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-10 19:19:23.716][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-10 19:19:23.725][biodb::testThat]
biodb.INFO [2023-04-10 19:19:23.726][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-10 19:19:23.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:23.739][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:23.744][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-04-10 19:19:23.746][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:23.750][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:23.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:23.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:23.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:23.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:23.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:23.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:23.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:23.787][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:23.789][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:23.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.791][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:23.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:23.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.809][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:23.810][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:23.811][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.812][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:23.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:23.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.851][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:23.853][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:23.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.856][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:23.867][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:23.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.870][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:23.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.879][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:23.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:23.882][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:23.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:23.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.892][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:23.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:23.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.896][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.898][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:23.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:23.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.904][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:23.906][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:23.907][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.909][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:23.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:23.919][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:23.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.922][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:23.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:23.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.930][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:23.931][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:23.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.934][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:23.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:23.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.943][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:23.945][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:23.946][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.947][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:23.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.956][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:23.957][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:23.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.960][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:23.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:23.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:23.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:23.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:23.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:23.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:23.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:23.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:23.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:24.124][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-04-10 19:19:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:24.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:24.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:24.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:24.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:24.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:24.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:24.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:24.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.390][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.393][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:24.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.467][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.470][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.487][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.495][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.497][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.498][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.522][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.523][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.525][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.551][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.553][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.569][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.573][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.577][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.578][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.580][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.581][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.596][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.604][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.605][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.607][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.624][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.628][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.631][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.632][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.650][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.654][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.658][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.659][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.660][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.661][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.662][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.691][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.693][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.717][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.720][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.733][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.736][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.737][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.742][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.743][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.745][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.750][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.751][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.753][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.758][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.761][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.761][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.767][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.768][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.769][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.770][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.783][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.785][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.786][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.792][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.793][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.794][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.795][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.800][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.802][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:24.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.803][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.810][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.813][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:24.820][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:24.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.822][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:24.828][biodb::testThat]
biodb.INFO [2023-04-10 19:19:24.829][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-10 19:19:24.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:24.831][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:24.846][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-04-10 19:19:24.855][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:24.859][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-04-10 19:19:24.860][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:24.862][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-04-10 19:19:24.863][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:24.885][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:24.887][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:24.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:24.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:24.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:24.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:24.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:24.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:24.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:24.901][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.904][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:24.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.932][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.934][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.936][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.937][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.941][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.942][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.944][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:24.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.949][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.950][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:24.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.957][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.958][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.960][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:24.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.965][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.966][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.968][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:24.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.974][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:24.975][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.976][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.985][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.990][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.991][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.992][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.993][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:24.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:24.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:24.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:24.998][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:24.999][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:25.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.001][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.003][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:25.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:25.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.006][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:25.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:25.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.009][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.011][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:25.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:25.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:25.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:25.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:25.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:25.052][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-04-10 19:19:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:25.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:25.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:25.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:25.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:25.071][biodb::testThat]
biodb.INFO [2023-04-10 19:19:25.072][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-10 19:19:25.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:25.073][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:25.076][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:25.077][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:25.078][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.079][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:25.080][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-04-10 19:19:25.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:25.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:25.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:25.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:25.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:25.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:25.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:25.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:25.124][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-04-10 19:19:25.129][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-10 19:19:25.157][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:25.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-10 19:19:25.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:25.175][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-10 19:19:25.196][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:25.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:25.201][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:25.202][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:26.184][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:26.749][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:26.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-04-10 19:19:26.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-04-10 19:19:26.781][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-04-10 19:19:26.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:26.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:26.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:26.828][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:26.829][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:26.831][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:26.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:26.834][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:26.837][biodb::testThat]
biodb.INFO [2023-04-10 19:19:26.839][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-10 19:19:26.840][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:26.842][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:26.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:26.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:26.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:26.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:26.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:26.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:26.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:26.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:26.968][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:26.975][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:26.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:19:26.980][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:26.982][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-04-10 19:19:27.010][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.012][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-10 19:19:27.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:27.015][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:27.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:27.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:27.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:27.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.078][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:27.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:27.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:27.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:27.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:27.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:27.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:27.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:27.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:27.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:27.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:27.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:27.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:27.199][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.201][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-10 19:19:27.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:27.204][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.215][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.217][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-10 19:19:27.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:27.220][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.228][biodb::testThat]
biodb.INFO [2023-04-10 19:19:27.230][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:27.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:27.233][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:27.238][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-04-10 19:19:27.821][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-04-10 19:19:29.078][biodb::testThat]
biodb.INFO [2023-04-10 19:19:29.080][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:29.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:29.082][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:29.526][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2023-04-10 19:19:30.913][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:30.915][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:30.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:30.919][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:30.920][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:30.922][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:30.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:30.925][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:30.928][biodb::testThat]
biodb.INFO [2023-04-10 19:19:30.929][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-04-10 19:19:30.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:30.932][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:30.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:30.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:30.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:30.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:30.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:30.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:30.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:30.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:30.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:31.106][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:31.110][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:31.112][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:19:31.114][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:31.115][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-10 19:19:31.181][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:31.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:31.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:19:31.188][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:31.189][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-04-10 19:19:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:31.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:31.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:31.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:31.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:31.282][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:31.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:32.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:32.122][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-04-10 19:19:32.129][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-04-10 19:19:32.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:32.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.145][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-04-10 19:19:32.189][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:32.191][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-04-10 19:19:32.193][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:32.194][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:32.195][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:32.196][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:32.197][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:32.198][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:32.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:32.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.212][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-04-10 19:19:32.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:32.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:32.217][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-04-10 19:19:32.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-04-10 19:19:33.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:33.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-04-10 19:19:33.058][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-04-10 19:19:33.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-04-10 19:19:33.063][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:33.065][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:33.066][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:33.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:33.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:33.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:33.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:33.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:33.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:33.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:33.094][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.097][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.102][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:33.104][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:33.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:33.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:33.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.111][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:33.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:33.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.114][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:33.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:33.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:33.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:33.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.123][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.128][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.129][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.131][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.137][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:33.138][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:33.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.140][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.141][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:33.142][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.143][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.144][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:33.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:33.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:33.152][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.153][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:33.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:33.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.158][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.159][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.160][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.161][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.167][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:33.168][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:33.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.170][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:33.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.176][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:33.177][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:33.178][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.179][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.180][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:33.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:33.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.224][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-04-10 19:19:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:33.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:33.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:33.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:33.253][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:33.664][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:34.092][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:34.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-04-10 19:19:34.101][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-04-10 19:19:34.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:34.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:34.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:34.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:34.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:34.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:34.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:34.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:34.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:34.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:34.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:34.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:34.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:34.180][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:34.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:34.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:34.190][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:34.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:35.023][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:35.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-04-10 19:19:35.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-04-10 19:19:35.075][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:35.081][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:35.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:19:35.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:35.088][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-10 19:19:35.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:35.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:35.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:35.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:35.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:35.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.150][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-04-10 19:19:35.151][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:35.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-04-10 19:19:35.154][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:35.155][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:35.156][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:35.157][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:35.158][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:35.159][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:35.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:35.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.185][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-04-10 19:19:35.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:35.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:35.190][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-04-10 19:19:35.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-04-10 19:19:36.014][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:36.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-04-10 19:19:36.024][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-04-10 19:19:36.028][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-04-10 19:19:36.050][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:36.053][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:36.055][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:36.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:36.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:36.080][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.085][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.094][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:36.095][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:36.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.098][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.100][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.107][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.110][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.111][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.117][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.119][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.124][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.126][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:36.128][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.130][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.134][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.136][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.137][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.139][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.141][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.144][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.153][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:36.154][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:36.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.158][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:36.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:36.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.167][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.168][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.170][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.172][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:36.240][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-04-10 19:19:36.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:36.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:36.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:36.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.293][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-04-10 19:19:36.294][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:36.296][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-04-10 19:19:36.297][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:36.299][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:36.300][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:36.301][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:36.302][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:36.303][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:36.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:36.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-04-10 19:19:36.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:36.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:36.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-04-10 19:19:36.735][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-04-10 19:19:37.163][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:37.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-04-10 19:19:37.172][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-04-10 19:19:37.177][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-04-10 19:19:37.179][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:37.181][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:37.183][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:37.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:37.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:37.208][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.210][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.213][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.220][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:37.222][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:37.223][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.224][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.226][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.227][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.229][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.230][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.232][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:37.234][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:37.235][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.236][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.240][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.242][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.244][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.246][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.249][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.250][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:37.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.255][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.258][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.261][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.263][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.264][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.266][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.267][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:37.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:37.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.281][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.283][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:37.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:37.292][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:37.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.295][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:37.353][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-04-10 19:19:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:37.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:37.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:37.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.385][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-04-10 19:19:37.386][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:37.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-04-10 19:19:37.390][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:37.391][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:37.392][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:37.393][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:37.394][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:37.395][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:37.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:37.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.418][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-04-10 19:19:37.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:37.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:37.424][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-04-10 19:19:37.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-04-10 19:19:38.268][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:38.272][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-04-10 19:19:38.275][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-04-10 19:19:38.278][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-04-10 19:19:38.280][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:38.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:38.282][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:38.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:38.297][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.300][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.305][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:38.306][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:38.307][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.308][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.309][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.310][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.311][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.312][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.314][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.315][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.316][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.319][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.320][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.322][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.323][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.324][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.324][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.326][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:38.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.329][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.330][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.331][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.333][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.335][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.338][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.344][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:38.345][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:38.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.347][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:38.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.352][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.355][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.396][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-04-10 19:19:38.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:38.427][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-04-10 19:19:38.428][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:38.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-04-10 19:19:38.430][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:38.431][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:38.432][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:38.433][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:38.434][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:38.435][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:38.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:38.459][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-04-10 19:19:38.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:38.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:38.465][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-04-10 19:19:38.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-04-10 19:19:39.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:39.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-04-10 19:19:39.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-04-10 19:19:39.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-04-10 19:19:39.508][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:39.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:39.512][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:39.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:39.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:39.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:39.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:39.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:39.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:39.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:39.535][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.537][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.540][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.547][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:39.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:39.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.551][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:39.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:39.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.559][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:39.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:39.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.563][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:39.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:39.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.572][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:39.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:39.575][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.577][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:39.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:39.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:39.587][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:39.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.590][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:39.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.598][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:39.600][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:39.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.603][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.605][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:39.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:39.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.612][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:39.614][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.620][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:39.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.627][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:39.629][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:39.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.632][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:39.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:39.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.641][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:39.642][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:39.644][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.645][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:39.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:39.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.654][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:39.656][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:39.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.659][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.662][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:39.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:39.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.669][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:39.670][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:39.672][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.673][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:39.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:39.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:39.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:39.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:39.719][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-04-10 19:19:39.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:39.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:39.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:39.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:39.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:39.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:39.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:39.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:39.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:39.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:39.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:39.757][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-04-10 19:19:39.758][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:39.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-04-10 19:19:39.762][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:39.763][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:39.764][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:39.765][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:39.766][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:39.767][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:39.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:39.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:39.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:39.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:39.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:39.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:39.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:39.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-04-10 19:19:39.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:39.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:39.788][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-04-10 19:19:40.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-04-10 19:19:40.628][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:40.632][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-04-10 19:19:40.636][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-04-10 19:19:40.639][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-04-10 19:19:40.640][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:40.642][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:40.643][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:40.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:40.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:40.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:40.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:40.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:40.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:40.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:40.659][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.660][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.661][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.662][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.667][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:40.668][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:40.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.670][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:40.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:40.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.676][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:40.677][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:40.678][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.679][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.681][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:40.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:40.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.685][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:40.686][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:40.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.688][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:40.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:40.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.693][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:40.694][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:40.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.696][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:40.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:40.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:40.703][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:40.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.704][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.706][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:40.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:40.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.710][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:40.711][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.712][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.713][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.714][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:40.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:40.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:40.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.721][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:40.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.726][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:40.727][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:40.728][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.729][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:40.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.734][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:40.735][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:40.736][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.737][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:40.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.742][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:40.743][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:40.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.745][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:40.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:40.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:40.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:40.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:40.799][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-04-10 19:19:40.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:40.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:40.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:40.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:40.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:40.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:40.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:40.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:40.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:40.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:40.824][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-04-10 19:19:40.825][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:40.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-04-10 19:19:40.828][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:40.829][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:40.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:40.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:40.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:40.833][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:40.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:40.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:40.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:40.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:40.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:40.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:40.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:40.850][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-04-10 19:19:40.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:40.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:40.856][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-04-10 19:19:41.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-04-10 19:19:41.682][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:41.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-04-10 19:19:41.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-04-10 19:19:41.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-04-10 19:19:41.697][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:41.698][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:41.700][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:41.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:41.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:41.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:41.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:41.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:41.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:41.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:41.716][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.719][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.725][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:41.726][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:41.727][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.728][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.733][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:41.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:41.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.736][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.737][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.741][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:41.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:41.743][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.744][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:41.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:41.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:41.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:41.751][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.752][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.759][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:41.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:41.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.764][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.765][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:41.767][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.768][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.770][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:41.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:41.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.782][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:41.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:41.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.790][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:41.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:41.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.795][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:41.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.819][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:41.821][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:41.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.824][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:41.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.832][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:41.834][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:41.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.837][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:41.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:41.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:41.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:41.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:41.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:41.904][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-04-10 19:19:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:41.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:41.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:41.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:41.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:41.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:41.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:41.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:41.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:41.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:41.948][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-04-10 19:19:41.949][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:41.951][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-04-10 19:19:41.952][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:41.953][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:41.954][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:41.956][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:41.957][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:41.958][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:41.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:41.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:41.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:41.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:41.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:41.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:41.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:41.974][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-04-10 19:19:41.978][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:41.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:41.982][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-04-10 19:19:42.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-04-10 19:19:42.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:42.845][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-04-10 19:19:42.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-04-10 19:19:42.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-04-10 19:19:42.857][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:42.858][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:42.860][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:42.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:42.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:42.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:42.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:42.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:42.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:42.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:42.907][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:42.910][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:42.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.913][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:42.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:42.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.922][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:42.923][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:42.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.926][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:42.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.935][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:42.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:42.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.940][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:42.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:42.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.948][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:42.949][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:42.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:42.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:42.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:42.962][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:42.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:42.965][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:42.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:43.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:43.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.006][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:43.007][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:43.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.009][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.010][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:43.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.013][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.015][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:43.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.019][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:43.020][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:43.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.022][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:43.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:43.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.028][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:43.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:43.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.032][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:43.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:43.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.038][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:43.039][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:43.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.041][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:43.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:43.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.047][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:43.048][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:43.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.050][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.051][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:43.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:43.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:43.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:43.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:43.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:43.106][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-04-10 19:19:43.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:43.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:43.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:43.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:43.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:43.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:43.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:43.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:43.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:43.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:43.136][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-04-10 19:19:43.137][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:43.139][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-04-10 19:19:43.141][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:43.142][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:43.143][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:43.144][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:43.145][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:43.146][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:43.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:43.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:43.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:43.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:43.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:43.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:43.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:43.160][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-04-10 19:19:43.162][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:43.163][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:43.165][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-04-10 19:19:43.577][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-04-10 19:19:44.005][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:44.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-04-10 19:19:44.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-04-10 19:19:44.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-04-10 19:19:44.017][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:44.018][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:44.020][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:44.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:44.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:44.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:44.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:44.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:44.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:44.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:44.033][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.034][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.036][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.049][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:44.050][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:44.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.052][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.053][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:44.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:44.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.057][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:44.057][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:44.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.059][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.060][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:44.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:44.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.064][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:44.065][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:44.066][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.067][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:44.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:44.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.072][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:44.073][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:44.074][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.075][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:44.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:44.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.080][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:44.081][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:44.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.082][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.083][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:44.085][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.086][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:44.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:44.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.094][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:44.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:44.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.099][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:44.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:44.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.101][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.106][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:44.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:44.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.109][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.110][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:44.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:44.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.114][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:44.115][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:44.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.117][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:44.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:44.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:44.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:44.157][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-04-10 19:19:44.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:44.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:44.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:44.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:44.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:44.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:44.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:44.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:44.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:44.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:44.179][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-04-10 19:19:44.180][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:44.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-04-10 19:19:44.182][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:44.183][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:44.184][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:44.185][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:44.186][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:44.187][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:44.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:44.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:44.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:44.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:44.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:44.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:44.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:44.200][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-04-10 19:19:44.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:44.203][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:44.205][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-04-10 19:19:44.620][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-04-10 19:19:45.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:45.060][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-04-10 19:19:45.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-04-10 19:19:45.066][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-04-10 19:19:45.067][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:45.069][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:45.070][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:45.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:45.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:45.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:45.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:45.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:45.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:45.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:45.083][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.086][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.091][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:45.092][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:45.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.093][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:45.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.098][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:45.099][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:45.100][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.101][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:45.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:45.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:45.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:45.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.109][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:45.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:45.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:45.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:45.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.117][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:45.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:45.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.121][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:45.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:45.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.124][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.125][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:45.126][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.128][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.129][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:45.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:45.134][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:45.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.136][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:45.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:45.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.140][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:45.141][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:45.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.143][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:45.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:45.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.148][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:45.149][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:45.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.151][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.152][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:45.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.156][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:45.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:45.158][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.159][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.160][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:45.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:45.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:45.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:45.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:45.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:45.202][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-04-10 19:19:45.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:45.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:45.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:45.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:45.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:45.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:45.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:45.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:45.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:45.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:45.225][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-04-10 19:19:45.226][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:45.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.INFO [2023-04-10 19:19:45.276][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-04-10 19:19:45.277][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:45.278][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:45.279][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:45.280][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:45.281][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:45.282][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:45.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:45.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:45.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:45.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:45.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:45.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:45.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:45.296][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-04-10 19:19:45.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:45.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:45.301][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-04-10 19:19:45.714][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-04-10 19:19:46.127][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:46.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-04-10 19:19:46.135][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-04-10 19:19:46.139][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-04-10 19:19:46.141][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:46.144][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:46.145][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:46.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:46.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:46.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:46.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:46.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:46.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:46.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:46.168][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.169][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.172][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.180][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:46.182][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:46.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.184][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.186][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:46.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:46.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.192][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:46.193][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:46.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.196][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:46.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:46.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.204][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:46.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:46.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.208][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:46.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:46.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.216][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:46.218][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:46.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.220][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:46.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:46.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.228][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:46.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:46.231][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.232][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.234][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:46.235][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.238][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.240][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:46.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:46.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:46.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.250][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:46.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.259][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:46.261][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:46.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.264][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:46.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:46.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.270][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:46.271][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:46.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.273][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.274][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:46.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:46.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:46.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.281][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:46.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:46.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:46.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:46.332][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-04-10 19:19:46.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:46.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:46.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:46.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:46.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:46.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:46.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:46.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:46.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:46.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:46.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:46.355][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-04-10 19:19:46.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:46.357][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-04-10 19:19:46.358][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:46.359][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:46.360][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:46.361][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:46.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:46.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:46.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:46.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:46.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:46.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:46.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:46.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:46.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:46.376][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-04-10 19:19:46.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:46.380][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:46.381][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-04-10 19:19:46.806][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-04-10 19:19:47.235][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:47.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-04-10 19:19:47.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-04-10 19:19:47.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-04-10 19:19:47.246][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:47.247][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:47.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:47.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:47.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:47.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:47.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:47.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:47.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:47.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:47.263][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.265][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.266][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.271][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:47.272][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:47.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.274][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.275][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:47.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:47.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.279][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:47.280][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:47.281][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.282][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:47.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:47.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.287][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:47.288][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:47.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.290][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.291][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:47.292][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:47.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.293][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.295][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:47.296][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:47.297][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.297][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.299][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:47.300][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.301][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.301][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.303][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:47.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:47.307][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:47.308][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.309][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:47.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:47.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.314][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:47.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:47.316][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.317][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:47.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:47.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.322][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:47.323][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:47.324][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.325][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.326][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:47.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:47.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.330][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:47.331][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:47.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.333][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:47.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:47.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:47.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:47.380][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-04-10 19:19:47.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:47.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:47.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:47.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:47.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:47.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:47.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:47.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:47.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:47.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:47.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:47.403][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-04-10 19:19:47.404][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:47.405][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-04-10 19:19:47.407][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:47.408][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:47.409][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:47.410][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:47.411][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:47.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:47.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:47.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:47.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:47.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:47.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:47.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:47.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:47.425][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-04-10 19:19:47.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:47.428][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:47.430][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-04-10 19:19:47.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-04-10 19:19:48.295][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-04-10 19:19:48.298][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-04-10 19:19:48.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-04-10 19:19:48.308][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-04-10 19:19:48.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-04-10 19:19:48.312][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:48.313][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:48.314][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:48.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:48.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:48.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:48.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:48.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:48.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:48.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:48.327][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.335][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:48.336][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:48.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.338][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.339][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:48.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:48.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.343][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:48.344][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:48.345][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.345][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:48.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:48.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.350][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:48.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:48.352][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.353][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:48.355][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:48.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.357][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.358][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:48.359][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:48.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.361][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.362][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:48.363][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.365][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.366][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:48.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:48.371][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:48.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.373][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:48.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.377][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:48.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:48.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.380][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:48.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:48.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.385][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:48.386][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:48.387][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.387][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.389][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:48.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:48.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.392][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:48.393][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:48.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:48.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:48.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:48.440][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-04-10 19:19:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:48.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:48.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:48.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:48.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:48.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:48.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:48.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:48.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:48.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:48.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:48.462][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-04-10 19:19:48.463][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:48.464][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-04-10 19:19:48.466][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:48.467][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:48.468][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:48.469][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:48.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:48.470][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:48.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:48.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:48.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:48.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:48.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:48.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:48.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:48.483][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-04-10 19:19:48.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:48.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:48.488][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-04-10 19:19:48.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-04-10 19:19:49.325][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:49.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-04-10 19:19:49.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-04-10 19:19:49.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-04-10 19:19:49.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:49.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:49.347][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:49.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:49.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:49.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:49.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:49.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:49.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:49.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:49.369][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.370][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.373][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.381][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:49.383][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:49.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.385][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.387][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:49.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:49.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.393][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:49.395][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:49.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.398][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:49.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:49.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:49.407][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.408][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:49.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:49.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:49.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:49.418][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.420][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:49.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:49.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.428][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:49.429][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:49.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.432][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.434][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:49.435][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.438][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.440][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:49.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:49.447][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:49.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.450][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:49.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.458][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:49.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:49.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.475][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:49.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:49.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.484][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:49.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:49.487][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.488][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:49.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.496][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:49.498][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:49.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.502][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:49.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:49.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:49.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:49.552][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-04-10 19:19:49.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:49.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:49.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:49.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:49.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:49.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:49.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:49.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:49.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:49.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:49.577][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-04-10 19:19:49.578][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:49.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-04-10 19:19:49.581][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:49.582][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:49.583][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:49.584][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:49.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:49.586][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:49.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:49.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:49.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:49.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:49.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:49.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:49.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:49.600][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-04-10 19:19:49.602][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:49.603][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:49.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-04-10 19:19:50.015][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-04-10 19:19:50.431][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:50.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-04-10 19:19:50.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-04-10 19:19:50.442][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-04-10 19:19:50.444][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:50.446][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:50.448][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:50.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:50.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:50.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:50.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:50.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:50.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:50.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:50.468][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.472][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.479][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:50.481][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:50.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.484][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.491][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:50.492][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:50.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.495][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:50.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:50.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:50.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.506][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.515][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:50.517][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:50.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.528][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:50.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.533][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:50.533][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:50.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.535][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.536][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:50.537][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.539][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.544][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:50.545][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:50.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.546][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:50.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:50.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.551][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:50.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:50.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.554][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:50.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:50.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:50.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.561][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.562][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.566][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:50.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:50.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.569][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:50.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:50.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:50.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:50.611][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-04-10 19:19:50.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:50.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:50.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:50.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:50.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:50.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:50.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:50.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:50.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:50.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:50.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:50.641][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-04-10 19:19:50.642][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:50.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-04-10 19:19:50.645][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:50.646][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:50.648][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:50.649][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:50.650][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:50.651][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:50.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:50.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:50.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:50.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:50.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:50.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:50.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:50.667][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-04-10 19:19:50.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:50.671][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:50.673][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-04-10 19:19:51.083][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-04-10 19:19:51.497][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:51.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-04-10 19:19:51.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-04-10 19:19:51.510][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-04-10 19:19:51.512][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:51.514][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:51.516][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:51.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:51.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:51.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:51.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:51.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:51.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:51.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:51.540][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.543][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.566][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:51.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:51.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.569][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:51.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:51.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.575][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:51.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:51.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.578][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:51.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:51.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.584][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:51.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:51.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.587][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:51.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:51.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.592][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:51.593][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:51.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.595][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:51.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:51.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.600][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:51.601][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:51.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.603][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.605][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:51.606][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.608][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.609][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.613][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:51.614][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:51.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:51.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.623][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:51.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:51.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.625][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:51.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:51.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.631][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:51.632][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:51.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:51.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:51.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.639][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:51.640][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:51.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.642][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.643][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:51.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:51.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:51.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:51.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:51.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:51.687][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-04-10 19:19:51.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:51.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:51.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:51.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:51.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:51.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:51.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:51.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:51.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:51.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:51.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:51.711][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-04-10 19:19:51.712][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:51.714][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-04-10 19:19:51.715][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:51.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:51.717][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:51.718][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:51.719][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:51.720][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:51.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:51.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:51.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:51.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:51.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:51.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:51.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:51.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-04-10 19:19:51.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:51.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:51.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-04-10 19:19:52.150][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-04-10 19:19:52.768][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:52.783][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-04-10 19:19:52.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-04-10 19:19:52.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-04-10 19:19:52.791][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:52.792][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:52.793][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:52.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:52.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:52.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:52.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:52.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:52.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:52.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:52.806][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.809][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.814][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:52.816][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:52.816][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.817][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.819][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:52.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:52.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.822][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:52.823][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:52.824][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.825][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:52.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:52.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.830][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:52.831][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:52.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.833][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:52.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.838][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:52.839][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:52.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.841][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:52.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.846][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:52.847][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:52.848][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.848][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.850][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:52.851][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.853][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:52.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.858][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:52.859][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:52.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.860][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:52.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:52.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.865][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:52.866][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:52.867][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.868][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:52.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:52.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.873][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:52.874][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:52.875][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.876][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:52.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:52.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:52.883][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:52.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.886][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:52.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:52.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:52.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:52.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:52.928][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-04-10 19:19:52.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:52.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:52.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:52.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:52.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:52.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:52.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:52.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:52.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:52.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:52.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:52.952][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-04-10 19:19:52.953][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:52.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-04-10 19:19:52.964][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:52.965][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:52.967][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:52.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:52.969][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:52.970][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:52.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:52.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:52.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:52.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:52.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:52.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:52.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:52.983][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-04-10 19:19:52.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:52.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:52.989][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-04-10 19:19:53.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-04-10 19:19:53.822][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:53.826][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-04-10 19:19:53.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-04-10 19:19:53.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-04-10 19:19:53.838][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:53.840][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:53.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:53.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:53.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:53.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:53.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:53.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:53.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:53.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:53.867][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:53.869][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:53.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.871][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:53.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.879][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:53.881][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:53.882][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.883][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:53.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.891][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:53.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:53.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.895][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:53.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.904][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:53.905][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:53.907][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.908][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.916][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:53.918][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:53.919][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.921][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:53.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:53.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.929][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:53.930][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:53.932][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.933][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.935][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:53.937][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:53.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.939][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:53.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.948][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:53.949][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:53.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.953][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:53.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:53.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.964][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:53.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:53.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.968][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:53.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:53.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.974][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:53.975][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:53.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.976][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:53.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:53.983][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:53.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.984][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:53.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:53.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:53.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:53.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:53.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:53.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:53.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:54.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:54.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:54.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:54.038][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-04-10 19:19:54.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:54.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:54.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:54.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:54.072][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:54.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:54.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:54.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:54.644][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:55.216][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:55.219][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-04-10 19:19:55.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-04-10 19:19:55.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:55.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:55.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:55.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:55.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:55.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:55.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:55.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:55.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:55.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:55.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:55.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:55.734][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:55.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:55.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:55.740][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:56.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:56.573][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:56.577][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-04-10 19:19:56.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-04-10 19:19:56.588][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:56.593][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:56.594][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:56.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:19:57.014][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:19:57.436][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:57.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-04-10 19:19:57.448][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-04-10 19:19:57.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:57.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:57.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:57.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:57.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:57.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:57.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:57.462][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-04-10 19:19:57.463][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:57.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-04-10 19:19:57.466][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:57.467][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:57.468][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:57.469][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:57.470][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:57.471][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:57.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:57.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:57.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:57.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:57.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:57.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:57.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:57.487][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-04-10 19:19:57.490][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:57.491][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:57.492][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-04-10 19:19:57.907][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-04-10 19:19:58.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:58.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-04-10 19:19:58.338][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-04-10 19:19:58.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-04-10 19:19:58.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:58.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:58.347][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:58.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:58.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:58.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:58.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:58.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:58.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:58.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:58.368][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.370][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.371][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.373][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.380][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:58.382][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:58.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.384][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:58.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.392][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:58.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:58.395][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.397][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:58.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:58.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:58.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:58.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.409][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:58.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:58.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.436][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:58.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:58.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.441][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:58.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:58.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.449][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:58.451][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:58.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.455][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.458][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:58.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:58.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.467][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:58.468][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:58.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.470][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.471][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:58.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:58.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.475][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.476][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.477][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.478][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.483][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:58.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:58.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.486][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:58.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:58.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:58.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:58.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.494][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:58.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:58.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.499][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:58.500][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:58.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.501][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:58.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:58.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:58.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:58.544][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-04-10 19:19:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:58.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:58.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:58.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:58.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:58.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:58.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:58.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:58.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:58.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:58.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:58.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:58.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:58.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:58.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:58.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:58.589][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-04-10 19:19:58.590][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:58.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-04-10 19:19:58.592][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:58.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:58.594][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:58.595][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:19:58.596][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:19:58.597][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:19:58.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:58.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:58.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:58.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:58.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:58.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:58.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:58.609][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-04-10 19:19:58.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:58.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:58.614][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-04-10 19:19:59.048][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-04-10 19:19:59.486][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:59.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-04-10 19:19:59.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-04-10 19:19:59.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-04-10 19:19:59.499][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:19:59.501][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:59.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:19:59.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.531][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.537][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.546][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:59.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:59.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.550][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:19:59.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:19:59.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.558][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:59.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:59.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.562][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.570][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:59.572][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:59.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.574][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:59.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:59.583][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:59.584][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.585][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:59.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.591][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:59.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:59.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.594][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.596][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:59.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:59.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.599][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:19:59.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:59.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.605][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.608][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.613][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:59.614][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:59.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.616][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.622][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:59.623][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:59.624][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.625][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:19:59.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:19:59.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.631][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:59.632][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:59.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:59.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:59.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:59.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.685][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-04-10 19:19:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.743][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:19:59.747][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:59.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:19:59.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:59.752][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-10 19:19:59.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:59.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:59.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:59.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:59.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:59.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:59.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:59.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:59.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:59.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.217][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:00.220][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:00.221][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-04-10 19:20:00.223][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:00.224][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-04-10 19:20:00.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:00.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:00.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.696][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:00.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:00.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:00.706][biodb::testThat]
biodb.INFO [2023-04-10 19:20:00.707][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-10 19:20:00.708][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:00.709][biodb::testThat]
biodb.TRACE[2023-04-10 19:20:00.712][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:20:00.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:20:00.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:00.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:00.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:00.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:00.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:00.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:00.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:00.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:00.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:00.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:00.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:00.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:00.752][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:00.753][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:00.754][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:01.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:01.580][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:01.583][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-04-10 19:20:01.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-04-10 19:20:01.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:01.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:01.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:01.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:01.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:01.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:01.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:01.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:01.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:01.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:01.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:01.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:01.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:01.634][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:01.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:01.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:01.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:05.061][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:05.475][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:05.478][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-04-10 19:20:05.484][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-04-10 19:20:05.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:05.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:05.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:05.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:05.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:05.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:05.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:05.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:05.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:05.523][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:05.528][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:05.529][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:05.532][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:05.950][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:06.369][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:06.372][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-04-10 19:20:06.378][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-04-10 19:20:06.383][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:06.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:06.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:06.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:06.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:06.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:06.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:06.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:06.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.414][private$selectFields]
biodb.TRACE[2023-04-10 19:20:06.415][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:06.416][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:06.418][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.423][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.425][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.426][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.429][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.430][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.431][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.434][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.437][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.438][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:06.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.469][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-10 19:20:06.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:06.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:06.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:06.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:06.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:06.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:06.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.497][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.498][private$selectFields]
biodb.TRACE[2023-04-10 19:20:06.498][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:06.499][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:06.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.502][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.504][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.505][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.507][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.509][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:06.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.513][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.514][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:06.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.536][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:06.538][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:06.539][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:06.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:06.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:06.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:06.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:06.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:06.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:06.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:06.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:06.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:06.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:06.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:06.633][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:07.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:07.492][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:07.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-04-10 19:20:07.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-04-10 19:20:07.507][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:07.511][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:07.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:07.516][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:07.933][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:08.349][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:08.352][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-04-10 19:20:08.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-04-10 19:20:08.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.479][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:08.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.522][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.523][private$selectFields]
biodb.TRACE[2023-04-10 19:20:08.524][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:08.525][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:08.526][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.527][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.528][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.529][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.530][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.533][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.535][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.536][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.539][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.540][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.552][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-10 19:20:08.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.610][private$selectFields]
biodb.TRACE[2023-04-10 19:20:08.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:08.612][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:08.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.621][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.632][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.634][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.635][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.636][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.637][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.649][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:08.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.676][private$selectFields]
biodb.TRACE[2023-04-10 19:20:08.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:08.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:08.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.682][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.688][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.689][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.690][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.691][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.692][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.694][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.695][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:08.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.709][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-10 19:20:08.710][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:08.711][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:08.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:08.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:08.728][biodb::testThat]
biodb.INFO [2023-04-10 19:20:08.729][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-10 19:20:08.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:08.731][biodb::testThat]
biodb.TRACE[2023-04-10 19:20:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:20:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:20:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:08.788][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:08.791][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:08.793][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-10 19:20:08.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:08.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-10 19:20:08.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.823][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:08.827][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:08.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-10 19:20:08.830][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:08.831][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-10 19:20:08.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:08.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:08.857][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:08.861][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:08.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-10 19:20:08.863][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:08.865][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-10 19:20:08.868][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:08.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.888][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.889][private$selectFields]
biodb.TRACE[2023-04-10 19:20:08.890][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:08.891][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:08.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.893][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.894][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.895][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.897][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.899][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.901][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.904][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.905][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.906][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:08.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.920][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-10 19:20:08.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:08.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:08.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:08.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:08.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:08.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:08.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:08.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.940][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.941][private$selectFields]
biodb.TRACE[2023-04-10 19:20:08.942][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:08.943][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:08.944][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.945][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.946][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.947][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.948][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.958][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.960][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:08.961][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.962][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.963][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.964][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:08.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:08.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.977][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:08.978][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:08.979][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:08.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:08.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:08.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:09.017][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.020][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.022][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-10 19:20:09.023][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.024][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-10 19:20:09.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.030][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-10 19:20:09.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.034][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-10 19:20:09.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.102][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:09.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.124][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.125][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.132][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.133][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.136][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.138][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.139][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.141][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.143][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.147][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.148][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-10 19:20:09.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.180][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.181][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.182][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.182][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.183][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.187][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.188][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.190][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.193][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.193][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.194][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.196][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.197][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.210][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:09.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.231][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.232][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.233][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.238][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.241][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.242][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.243][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.244][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.245][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.246][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.247][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.248][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-10 19:20:09.262][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:09.262][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:09.270][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:09.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:09.275][biodb::testThat]
biodb.INFO [2023-04-10 19:20:09.276][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-10 19:20:09.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:09.278][biodb::testThat]
biodb.TRACE[2023-04-10 19:20:09.281][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:20:09.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:20:09.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:09.322][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.325][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.327][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-04-10 19:20:09.328][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.330][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-04-10 19:20:09.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.355][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.358][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-04-10 19:20:09.360][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.362][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-04-10 19:20:09.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.387][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-04-10 19:20:09.392][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.393][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-04-10 19:20:09.396][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:09.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.416][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.417][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.418][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.419][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.423][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.424][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.425][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.426][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.428][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.429][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.430][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.431][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.432][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.433][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.446][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-04-10 19:20:09.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.464][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.465][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.466][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.466][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.471][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.481][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.482][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.484][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.485][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.486][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.486][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.487][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.499][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:09.500][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:09.501][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:09.552][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.555][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.556][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-04-10 19:20:09.557][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.558][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-04-10 19:20:09.561][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:09.564][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:09.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-04-10 19:20:09.567][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:09.568][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-04-10 19:20:09.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:09.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:09.637][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:09.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.664][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.665][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.666][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.667][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.672][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.672][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.673][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.674][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.676][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.677][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.678][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.679][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.681][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.682][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.683][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.696][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-04-10 19:20:09.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.715][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.716][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.717][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.718][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.718][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.721][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.722][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.723][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.724][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.725][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.727][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.731][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.732][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.744][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-04-10 19:20:09.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:09.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.763][private$selectFields]
biodb.TRACE[2023-04-10 19:20:09.764][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:09.765][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:09.766][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.767][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.768][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.769][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.769][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.772][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.773][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-04-10 19:20:09.776][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.777][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.778][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.779][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-04-10 19:20:09.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:09.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:09.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-04-10 19:20:09.792][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:09.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:09.817][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:09.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:09.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:09.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:09.823][biodb::testThat]
biodb.INFO [2023-04-10 19:20:09.824][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-10 19:20:09.825][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:09.826][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:09.828][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-10 19:20:09.829][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:20:09.831][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-10 19:20:09.832][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:20:09.833][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:09.834][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:09.835][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:09.836][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:09.837][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:09.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:09.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:09.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:09.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:09.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:09.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:09.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:09.850][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-04-10 19:20:09.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:09.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:09.856][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-04-10 19:20:10.276][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-04-10 19:20:10.769][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:10.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-04-10 19:20:10.779][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-04-10 19:20:10.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-04-10 19:20:10.783][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:20:10.784][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:20:10.786][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:20:10.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:10.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:10.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:10.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:10.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:10.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:10.799][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.801][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.802][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.808][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:10.809][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:10.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.810][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.812][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:10.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:10.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.814][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.816][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:10.817][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:10.818][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.819][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.820][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:10.821][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:10.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.823][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.824][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:10.825][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:10.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.827][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.828][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:10.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:10.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.831][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:10.833][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:10.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.835][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.836][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:10.837][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:10.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.839][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.840][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:10.841][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:10.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.843][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:10.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:10.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.847][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:10.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:10.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:10.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:10.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:10.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:10.887][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-04-10 19:20:10.888][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-10 19:20:10.894][biodb::testThat]
biodb.INFO [2023-04-10 19:20:10.896][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-10 19:20:10.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:10.897][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:10.915][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-04-10 19:20:10.916][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-04-10 19:20:10.917][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-04-10 19:20:10.919][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-04-10 19:20:10.920][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-04-10 19:20:10.921][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:10.922][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:10.923][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:10.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:10.925][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:10.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:10.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:10.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:10.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:10.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:10.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:10.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:10.940][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-04-10 19:20:10.942][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:10.943][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:10.945][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-04-10 19:20:11.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-04-10 19:20:11.831][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:11.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-04-10 19:20:11.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-04-10 19:20:11.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:11.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:11.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:11.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:11.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:11.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:11.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:11.855][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-04-10 19:20:11.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:11.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:11.860][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-04-10 19:20:12.295][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-04-10 19:20:12.713][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:12.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-04-10 19:20:12.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-04-10 19:20:12.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:12.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:12.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:12.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:12.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:12.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:12.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:12.739][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-04-10 19:20:12.743][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:12.744][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:12.746][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-04-10 19:20:13.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-04-10 19:20:13.572][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:13.576][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-04-10 19:20:13.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-04-10 19:20:13.586][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-04-10 19:20:13.589][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:20:13.591][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-04-10 19:20:13.593][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-04-10 19:20:13.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:13.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:13.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:13.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:13.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:13.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:13.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:13.616][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.618][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.621][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.629][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:13.631][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:13.632][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.635][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:13.637][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:13.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.640][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.642][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:13.643][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:13.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.646][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.648][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.649][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.651][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.652][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.654][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.658][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.660][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:13.662][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:13.663][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.665][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.671][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.673][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:13.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:13.676][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.677][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.679][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:13.681][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:13.682][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.686][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:13.687][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:13.689][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.690][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:13.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:13.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:13.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:13.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:13.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:13.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:13.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:13.769][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.778][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:13.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:13.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.781][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.787][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:13.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:13.789][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.790][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.796][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:13.797][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:13.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.799][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:13.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.807][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.808][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.810][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.816][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.817][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.818][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.820][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.826][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:13.828][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:13.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.830][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.838][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.844][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:13.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:13.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.846][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:13.853][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:13.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.855][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.860][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:13.861][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:13.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.863][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:13.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:13.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:13.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:13.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:13.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:13.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:13.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:13.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:13.912][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.915][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.915][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.921][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:13.922][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:13.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.924][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.939][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:13.941][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.943][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:13.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:13.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.948][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:13.949][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:13.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.951][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:13.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:13.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.956][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.957][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.958][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.959][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:13.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.964][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.965][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.966][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.967][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:13.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.972][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:13.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:13.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.975][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.977][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:13.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:13.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.981][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.982][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.983][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.984][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:13.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.989][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:13.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:13.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:13.992][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:13.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:13.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.003][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:14.004][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:14.005][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.006][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.013][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:14.014][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:14.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.016][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.017][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:14.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:14.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:14.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:14.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:14.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:14.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:14.092][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-04-10 19:20:14.093][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-10 19:20:14.094][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-10 19:20:14.108][biodb::testThat]
biodb.INFO [2023-04-10 19:20:14.109][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-10 19:20:14.110][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:14.111][biodb::testThat]
biodb.INFO [2023-04-10 19:20:14.152][biodb::testThat]
biodb.INFO [2023-04-10 19:20:14.153][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-10 19:20:14.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:14.156][biodb::testThat]
biodb.INFO [2023-04-10 19:20:14.163][biodb::testThat]
biodb.INFO [2023-04-10 19:20:14.164][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-10 19:20:14.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:14.166][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:14.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:14.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:14.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:14.176][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:14.677][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:15.432][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:15.436][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-04-10 19:20:15.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-04-10 19:20:15.451][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:15.453][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:15.454][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:15.455][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:15.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:15.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:15.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:15.459][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:15.460][biodb::testThat]
biodb.INFO [2023-04-10 19:20:15.461][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-10 19:20:15.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:15.463][biodb::testThat]
biodb.ERROR[2023-04-10 19:20:15.478][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-10 19:20:15.495][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-10 19:20:15.506][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:20:15.508][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-10 19:20:15.509][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-10 19:20:15.510][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:20:15.510][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:15.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:15.512][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.514][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:20:15.525][biodb::testContext]
biodb.INFO [2023-04-10 19:20:15.527][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:15.528][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-04-10 19:20:15.529][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:15.530][biodb::testContext]
biodb.INFO [2023-04-10 19:20:15.532][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:15.533][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:15.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:15.539][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:20:15.540][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.543][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:20:15.544][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.548][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:20:15.549][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.553][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:20:15.554][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:20:15.555][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:20:15.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.559][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:20:15.560][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:20:15.561][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.565][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:20:15.566][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:20:15.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.570][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:20:15.571][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:20:15.572][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:20:15.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.576][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:20:15.577][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.593][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:20:15.594][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:20:15.595][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:20:15.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.599][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:15.600][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:20:15.601][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:20:15.602][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:20:15.603][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:20:15.604][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:20:15.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.608][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:20:15.609][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:20:15.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.613][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:20:15.614][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:20:15.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.618][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:20:15.619][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:20:15.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.623][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:20:15.624][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:20:15.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.627][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:20:15.628][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:20:15.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.632][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:15.633][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:20:15.638][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:20:15.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.642][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:20:15.643][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:20:15.645][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:20:15.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.648][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:20:15.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.677][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:20:15.678][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.679][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:15.680][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.682][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.683][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.684][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:15.685][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:15.686][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.687][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:20:15.688][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:15.689][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.690][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.691][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:15.691][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:15.691][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:15.691][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:15.691][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:15.692][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:15.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.695][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:15.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.699][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.700][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:15.700][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:15.701][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.702][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.703][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:20:15.705][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.706][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:15.707][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.708][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:15.709][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.710][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.711][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.713][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:15.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:15.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.716][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:20:15.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:15.718][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.719][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.720][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:15.720][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:15.720][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:15.720][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:15.720][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:15.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:15.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:15.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.726][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.727][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:15.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:15.730][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.732][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.733][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:20:15.735][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:20:15.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:15.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.742][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.743][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:15.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:15.745][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.746][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:20:15.747][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:15.748][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.749][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.750][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.751][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:15.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:15.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.765][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:15.768][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:15.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.769][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.770][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:20:15.772][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.773][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:15.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.775][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:15.776][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.777][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.778][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.779][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.780][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:15.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:15.782][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.783][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:20:15.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:15.785][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:15.787][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:15.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:15.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:15.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:15.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:15.794][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:15.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:15.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:15.798][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:15.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:15.800][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.878][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:20:15.879][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:20:15.881][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:20:15.882][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:20:15.883][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:15.885][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:20:15.886][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:15.888][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:15.889][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:20:15.890][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:20:15.892][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:15.893][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:20:15.894][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:15.896][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:15.897][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:20:15.898][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:20:15.900][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:20:15.901][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:20:15.902][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:15.904][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:20:15.905][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:20:15.906][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:20:15.908][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:20:15.909][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:20:15.910][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:20:15.912][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:20:15.913][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:20:15.914][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:20:15.916][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:20:15.917][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:20:15.918][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:20:15.920][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:20:15.921][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:20:15.922][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:20:15.924][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:20:15.925][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:20:15.933][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:20:15.935][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:20:15.936][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:20:15.938][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:20:15.939][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:20:15.940][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:20:15.942][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:20:15.943][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:20:15.944][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:20:15.946][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:20:15.947][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:20:15.948][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:20:15.950][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:20:15.951][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:20:15.952][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:20:15.954][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:20:15.955][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:20:15.957][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:20:15.958][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:20:15.959][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:20:15.961][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:20:15.962][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:20:15.964][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:20:15.965][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:20:15.966][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:20:15.968][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:20:15.969][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:20:15.970][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:20:15.971][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:20:15.973][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:20:15.974][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:15.975][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:15.977][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:20:15.978][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:20:15.979][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:20:15.981][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:20:15.982][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:20:15.983][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:20:15.985][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:20:15.986][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:20:15.987][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:20:15.988][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:20:15.990][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:20:15.991][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:20:15.992][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:20:15.994][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:20:15.995][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:20:15.996][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:20:15.998][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:15.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:16.000][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.002][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:16.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:16.112][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:16.113][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-10 19:20:16.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:16.116][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:20:16.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:16.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:16.119][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:16.120][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:16.121][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:16.122][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-10 19:20:16.123][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:20:16.124][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:16.125][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:16.125][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-10 19:20:16.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-10 19:20:16.127][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-10 19:20:16.128][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:16.129][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:16.129][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:16.129][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:16.130][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:20:16.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:16.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:16.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:16.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:16.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:16.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:16.136][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:16.136][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-10 19:20:16.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:16.138][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:16.139][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:16.140][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-10 19:20:16.140][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-10 19:20:16.141][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:16.143][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:16.144][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-10 19:20:16.146][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:16.147][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:16.149][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:16.152][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-10 19:20:16.153][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-10 19:20:16.154][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-10 19:20:16.155][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-10 19:20:16.157][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:16.158][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:16.159][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-10 19:20:16.160][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-10 19:20:16.161][biodb::testThat]
biodb.INFO [2023-04-10 19:20:16.162][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-04-10 19:20:16.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:16.164][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:16.168][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-10 19:20:16.171][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:16.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:16.173][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-04-10 19:20:16.583][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-04-10 19:20:17.190][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:17.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-04-10 19:20:17.200][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-04-10 19:20:17.204][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:17.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:17.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:17.209][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:18.235][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:18.649][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:18.652][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-04-10 19:20:18.657][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-04-10 19:20:18.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:18.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:18.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:18.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:18.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:18.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:18.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:18.673][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:18.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:18.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:18.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:19.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:19.569][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:19.573][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-04-10 19:20:19.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-04-10 19:20:19.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:19.663][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:19.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-10 19:20:19.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:19.669][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-10 19:20:19.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.689][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:19.692][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:19.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-10 19:20:19.695][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:19.696][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-10 19:20:19.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:19.728][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:19.729][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-04-10 19:20:19.731][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:19.732][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-04-10 19:20:19.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:19.753][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:19.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-04-10 19:20:19.757][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:19.758][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-04-10 19:20:19.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:19.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:19.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:19.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:19.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:19.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:19.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:19.773][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:19.777][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:19.779][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:19.782][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:20.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:20.623][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:20.627][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-04-10 19:20:20.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-04-10 19:20:20.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:20.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:20.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:20.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:20.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:20.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:20.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:20:20.649][biodb::testThat]
biodb.INFO [2023-04-10 19:20:20.650][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-04-10 19:20:20.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:20.652][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:20.656][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:20.659][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:20.660][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:20.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:21.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:21.520][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:21.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-04-10 19:20:21.533][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-04-10 19:20:21.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:21.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:21.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:21.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:21.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:21.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:21.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:21.561][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:21.565][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:21.566][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:21.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:21.982][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:22.405][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:22.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-04-10 19:20:22.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-04-10 19:20:22.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:22.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:22.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:22.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:20:22.432][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:20:22.433][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-10 19:20:22.434][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-10 19:20:22.435][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:20:22.436][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:22.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:22.438][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.439][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:20:22.444][biodb::testContext]
biodb.INFO [2023-04-10 19:20:22.445][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:22.446][biodb::testContext] Test context - Test web services
biodb.INFO [2023-04-10 19:20:22.447][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:22.448][biodb::testContext]
biodb.INFO [2023-04-10 19:20:22.450][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:22.452][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:22.456][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:22.457][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:20:22.458][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.461][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:20:22.462][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.466][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:20:22.467][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.470][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:20:22.471][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:20:22.473][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:20:22.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.476][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:20:22.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:20:22.478][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.482][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:20:22.483][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:20:22.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.487][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:20:22.488][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:20:22.489][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:20:22.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.493][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:20:22.494][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.498][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:20:22.499][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:20:22.500][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:20:22.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.504][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:22.505][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:20:22.506][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:20:22.507][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:20:22.508][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:20:22.510][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:20:22.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.514][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:20:22.515][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:20:22.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.519][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:20:22.520][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:20:22.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.524][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:20:22.525][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:20:22.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.529][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:20:22.530][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:20:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.535][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:20:22.536][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:20:22.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.541][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:22.542][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:20:22.547][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:20:22.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.553][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:20:22.555][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:20:22.556][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:20:22.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.560][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:20:22.562][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.563][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:20:22.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:22.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.570][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:22.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:22.572][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.573][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:20:22.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:22.575][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.576][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.577][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:22.577][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:22.577][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:22.577][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:22.577][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:22.578][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:22.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.581][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:22.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.794][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.795][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:22.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:22.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.798][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.799][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:20:22.801][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:22.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:22.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.806][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.808][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:22.809][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:22.810][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.811][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:20:22.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:22.813][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.815][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:22.815][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:22.815][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:22.815][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:22.815][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:22.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:22.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:22.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.822][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.823][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:22.824][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:22.825][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.826][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.827][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:20:22.829][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.830][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:20:22.831][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.832][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:22.833][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.834][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.835][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.836][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:22.837][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:22.838][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.839][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:20:22.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:22.841][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.842][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.843][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.844][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:22.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.846][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:22.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.850][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:22.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:22.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.854][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.855][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:20:22.857][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.858][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:22.858][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.859][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:22.860][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.861][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.862][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.864][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:22.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:22.866][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.867][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:20:22.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:22.869][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.870][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:22.871][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:22.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.874][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:22.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:22.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:22.877][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:22.878][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:22.879][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:22.880][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:22.881][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:22.882][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:22.883][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:22.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:22.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:22.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:22.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:22.960][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:20:22.961][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:20:22.963][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:20:22.964][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:20:22.965][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:22.967][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:20:22.968][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:22.969][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:22.970][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:20:22.972][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:20:22.973][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:22.974][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:20:22.975][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:22.977][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:22.978][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:20:22.979][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:20:22.980][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:20:22.981][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:20:22.982][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:22.984][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:20:22.985][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:20:22.986][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:20:22.987][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:20:22.989][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:20:22.990][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:20:22.991][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:20:22.992][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:20:22.994][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:20:22.995][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:20:22.996][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:20:22.997][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:20:22.998][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:20:23.000][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:20:23.001][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:20:23.002][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:20:23.003][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:20:23.004][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:20:23.006][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:20:23.007][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:20:23.008][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:20:23.009][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:20:23.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:20:23.012][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:20:23.013][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:20:23.014][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:20:23.016][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:20:23.017][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:20:23.018][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:20:23.019][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:20:23.020][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:20:23.022][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:20:23.023][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:20:23.024][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:20:23.025][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:20:23.027][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:20:23.028][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:20:23.029][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:20:23.030][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:20:23.032][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:20:23.033][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:20:23.034][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:20:23.035][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:20:23.037][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:20:23.038][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:20:23.039][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:20:23.040][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:20:23.042][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:23.043][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:23.044][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:20:23.045][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:20:23.047][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:20:23.048][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:20:23.049][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:20:23.050][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:20:23.052][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:20:23.053][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:20:23.054][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:20:23.056][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:20:23.057][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:20:23.058][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:20:23.059][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:20:23.061][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:20:23.062][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:20:23.063][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:20:23.065][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:23.066][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:23.066][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.068][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:23.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:23.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:23.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:23.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:23.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:23.173][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:23.174][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-10 19:20:23.176][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:23.177][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:20:23.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:23.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:23.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:23.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:23.181][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:23.182][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-10 19:20:23.182][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:20:23.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:23.184][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:23.185][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-10 19:20:23.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-10 19:20:23.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-10 19:20:23.188][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:23.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:23.189][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:23.189][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:23.190][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:20:23.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:23.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:23.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:23.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:23.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:23.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:23.195][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:23.195][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-10 19:20:23.196][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:23.197][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:23.198][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:23.199][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-10 19:20:23.199][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-10 19:20:23.200][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:23.201][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:23.202][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-10 19:20:23.204][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:23.205][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:23.206][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:23.209][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-10 19:20:23.210][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-10 19:20:23.211][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-10 19:20:23.213][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-10 19:20:23.214][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:23.214][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:23.216][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-10 19:20:23.217][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-10 19:20:23.218][biodb::testThat]
biodb.INFO [2023-04-10 19:20:23.219][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-04-10 19:20:23.220][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:23.221][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:23.224][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-10 19:20:23.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:23.228][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-10 19:20:23.230][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:23.231][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-10 19:20:23.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:23.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:23.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:23.239][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-04-10 19:20:25.477][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-04-10 19:20:25.896][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:25.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-04-10 19:20:25.906][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-04-10 19:20:25.914][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:20:25.916][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-10 19:20:25.918][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-10 19:20:25.920][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:20:25.921][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:25.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:25.924][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:25.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:25.926][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:25.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:20:25.934][biodb::testContext]
biodb.INFO [2023-04-10 19:20:25.935][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:25.936][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-04-10 19:20:25.938][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:20:25.939][biodb::testContext]
biodb.INFO [2023-04-10 19:20:25.942][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:25.944][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:25.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:25.951][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:20:25.952][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:20:25.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:25.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:25.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:25.958][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:20:25.959][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:20:25.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:25.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:25.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:25.977][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:20:25.978][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:20:25.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:25.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:25.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:25.983][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:20:25.985][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:20:25.986][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:20:25.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:25.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:25.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:25.992][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:20:25.994][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:20:25.996][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:20:25.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:25.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.002][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:20:26.003][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:20:26.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.009][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:20:26.010][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:20:26.012][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:20:26.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.020][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:20:26.023][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:20:26.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.028][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:20:26.029][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:20:26.030][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:20:26.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.034][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:26.035][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:20:26.035][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:20:26.036][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:20:26.037][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:20:26.038][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:20:26.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.042][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:20:26.043][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:20:26.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.046][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:20:26.047][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:20:26.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.050][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:20:26.051][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:20:26.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.054][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:20:26.056][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:20:26.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.059][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:20:26.060][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:20:26.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.063][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:20:26.064][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:20:26.069][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:20:26.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.073][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:20:26.074][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:20:26.075][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:20:26.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.078][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:20:26.080][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.081][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:20:26.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.083][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:26.084][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.085][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.086][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.087][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:26.088][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:26.089][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.090][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:20:26.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:26.092][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.093][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.094][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:26.094][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:26.094][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:26.094][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:26.094][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:26.095][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:26.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.097][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:26.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.101][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:26.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:26.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.104][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.105][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:20:26.107][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.108][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:26.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.110][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:26.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.113][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.115][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:26.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:26.117][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.118][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:20:26.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:26.119][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.120][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.121][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:26.121][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:26.121][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:26.121][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:20:26.121][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:20:26.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:26.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:26.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.129][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:26.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:26.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.132][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.133][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:20:26.135][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.136][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:20:26.137][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.138][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:26.139][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.140][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.141][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.142][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.143][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:20:26.144][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:26.145][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.146][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:20:26.147][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:26.148][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.149][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.150][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.151][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:26.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.154][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:26.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.158][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:26.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:26.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.167][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.168][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:20:26.170][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.171][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:20:26.172][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.173][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:26.173][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.175][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.176][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.177][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:20:26.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:26.179][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.180][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:20:26.181][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:26.182][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.183][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.184][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:20:26.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:26.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.191][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:26.192][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:26.193][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.194][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:20:26.196][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:26.196][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.266][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:20:26.268][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:20:26.269][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:20:26.270][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:20:26.272][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:26.273][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:20:26.274][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:26.276][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:26.277][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:20:26.278][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:20:26.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:26.281][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:20:26.282][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:20:26.284][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:20:26.285][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:20:26.286][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:20:26.287][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:20:26.289][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:20:26.290][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:26.291][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:20:26.292][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:20:26.294][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:20:26.295][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:20:26.296][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:20:26.298][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:20:26.299][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:20:26.300][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:20:26.302][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:20:26.303][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:20:26.304][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:20:26.305][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:20:26.307][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:20:26.308][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:20:26.309][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:20:26.310][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:20:26.312][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:20:26.313][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:20:26.314][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:20:26.316][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:20:26.317][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:20:26.318][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:20:26.320][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:20:26.321][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:20:26.329][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:20:26.331][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:20:26.332][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:20:26.334][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:20:26.335][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:20:26.336][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:20:26.338][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:20:26.339][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:20:26.340][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:20:26.341][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:20:26.343][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:20:26.344][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:20:26.345][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:20:26.347][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:20:26.348][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:20:26.349][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:20:26.350][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:20:26.352][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:20:26.353][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:20:26.354][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:20:26.355][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:20:26.357][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:20:26.358][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:20:26.359][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:26.360][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:26.362][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:20:26.363][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:20:26.364][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:20:26.366][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:20:26.367][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:20:26.368][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:20:26.370][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:20:26.371][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:20:26.372][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:20:26.374][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:20:26.375][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:20:26.376][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:20:26.378][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:20:26.379][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:20:26.380][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:20:26.382][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:20:26.384][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:20:26.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:20:26.386][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.387][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:20:26.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.497][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-04-10 19:20:26.498][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-04-10 19:20:26.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.501][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.502][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:20:26.503][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.504][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.505][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.506][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-04-10 19:20:26.507][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:20:26.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:20:26.509][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.510][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-04-10 19:20:26.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-04-10 19:20:26.511][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-04-10 19:20:26.512][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:20:26.513][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:20:26.513][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:20:26.513][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:20:26.514][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:20:26.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:20:26.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:20:26.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:20:26.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:20:26.520][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:26.520][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-04-10 19:20:26.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:20:26.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:20:26.522][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:20:26.523][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-04-10 19:20:26.523][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-04-10 19:20:26.525][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:20:26.526][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:20:26.527][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-04-10 19:20:26.529][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:20:26.530][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:20:26.531][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:20:26.534][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-04-10 19:20:26.535][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-04-10 19:20:26.536][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-04-10 19:20:26.538][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-04-10 19:20:26.539][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:26.540][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:20:26.541][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-04-10 19:20:26.542][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-04-10 19:20:26.543][biodb::testThat]
biodb.INFO [2023-04-10 19:20:26.544][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-04-10 19:20:26.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:26.545][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:26.549][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-04-10 19:20:26.557][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:26.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-04-10 19:20:26.560][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:26.562][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-04-10 19:20:26.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-04-10 19:20:26.571][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:26.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-04-10 19:20:26.574][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:26.575][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-04-10 19:20:26.579][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-04-10 19:20:26.580][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:20:26.582][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-04-10 19:20:26.583][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:20:26.584][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:26.585][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:26.586][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-04-10 19:20:26.587][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:26.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:26.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:26.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:26.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:26.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:26.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:26.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:26.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:26.604][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-04-10 19:20:26.607][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:26.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:26.609][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-04-10 19:20:27.036][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-04-10 19:20:27.843][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:27.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-04-10 19:20:27.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-04-10 19:20:27.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-04-10 19:20:27.858][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:20:27.860][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:20:27.861][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-04-10 19:20:27.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:27.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:27.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:27.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:27.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:27.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:27.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:27.877][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:27.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:27.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.881][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:27.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.899][ef$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:27.900][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:27.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.902][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.903][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-04-10 19:20:27.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-04-10 19:20:27.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.907][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:27.908][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:27.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.910][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:27.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.929][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:20:27.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:20:27.932][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.933][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:20:27.935][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:20:27.936][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.937][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.938][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:27.939][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:27.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.941][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.943][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:27.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:27.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.946][ef$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:27.948][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:27.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.949][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-04-10 19:20:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:27.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:27.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:27.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.958][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:27.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:27.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.963][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:27.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:27.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.966][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:27.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:27.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.971][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:27.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:27.973][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.974][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-04-10 19:20:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-04-10 19:20:27.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.980][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:27.981][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:27.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.983][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:20:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:20:27.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:27.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:27.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:27.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:27.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:28.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:28.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:28.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:28.024][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-04-10 19:20:28.026][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:20:28.027][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-04-10 19:20:28.028][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-04-10 19:20:28.029][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:20:28.029][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:28.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:28.031][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:28.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:28.033][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:28.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
19.186 0.707 67.377
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.148 | 0.153 | 6.473 | |
| ChebiEntry | 0.38 | 0.00 | 0.38 | |