Back to Multiple platform build/check report for BioC 3.19:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-18 11:35:50 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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

Package 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbChebi on nebbiolo1


To the developers/maintainers of the biodbChebi package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbChebi
Version: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-05-17 20:36:47 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 20:38:07 -0400 (Fri, 17 May 2024)
EllapsedTime: 80.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* 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 code 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 [2024-05-17 20:37:31.094][biodb::testContext]
biodb.INFO [2024-05-17 20:37:31.097][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:31.098][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-17 20:37:31.099][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:31.100][biodb::testContext]
biodb.INFO [2024-05-17 20:37:31.109][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:31.112][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:31.122][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:31.123][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 20:37:31.124][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.128][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 20:37:31.150][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.155][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 20:37:31.156][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.160][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 20:37:31.161][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 20:37:31.162][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 20:37:31.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.166][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 20:37:31.167][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 20:37:31.168][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.172][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 20:37:31.173][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 20:37:31.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.177][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 20:37:31.178][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 20:37:31.179][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 20:37:31.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.183][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 20:37:31.185][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.189][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 20:37:31.190][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 20:37:31.191][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 20:37:31.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.195][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:31.196][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 20:37:31.197][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 20:37:31.198][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 20:37:31.199][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 20:37:31.200][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 20:37:31.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.204][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 20:37:31.205][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 20:37:31.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.209][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 20:37:31.210][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 20:37:31.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.213][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[2024-05-17 20:37:31.214][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 20:37:31.215][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 20:37:31.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.219][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 20:37:31.220][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 20:37:31.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.224][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 20:37:31.225][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 20:37:31.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.229][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:31.230][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 20:37:31.235][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 20:37:31.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.238][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[2024-05-17 20:37:31.239][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 20:37:31.240][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 20:37:31.241][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 20:37:31.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.248][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 20:37:31.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.336][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 20:37:31.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:31.342][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.347][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:31.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:31.350][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.351][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 20:37:31.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:31.354][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.357][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:31.357][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:31.357][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:31.357][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:31.357][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:31.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:31.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:31.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.365][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.366][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:31.367][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:31.368][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.369][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.371][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 20:37:31.372][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.374][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:31.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.376][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:31.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.381][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:31.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:31.383][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.384][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 20:37:31.385][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:31.386][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:31.387][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:31.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:31.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:31.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.394][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.395][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:31.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:31.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.398][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.399][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 20:37:31.401][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.402][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 20:37:31.403][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.404][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:31.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.409][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:31.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:31.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.412][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 20:37:31.413][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:31.413][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.415][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:31.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:31.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.423][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:31.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:31.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.426][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.427][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 20:37:31.429][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.430][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:31.431][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.432][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:31.433][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.435][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.436][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:31.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:31.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.439][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 20:37:31.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:31.441][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.442][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.443][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.444][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:31.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:31.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.449][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.450][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:31.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:31.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.454][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:31.458][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:31.459][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.460][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[2024-05-17 20:37:31.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.472][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[2024-05-17 20:37:31.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.481][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[2024-05-17 20:37:31.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.485][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[2024-05-17 20:37:31.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.515][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.DEBUG[2024-05-17 20:37:31.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.523][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[2024-05-17 20:37:31.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.528][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[2024-05-17 20:37:31.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.533][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 20:37:31.538][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 20:37:31.539][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 20:37:31.540][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 20:37:31.542][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:31.543][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 20:37:31.544][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:31.546][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:31.547][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 20:37:31.548][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 20:37:31.550][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:31.551][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 20:37:31.552][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:31.553][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:31.555][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 20:37:31.556][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 20:37:31.557][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 20:37:31.559][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 20:37:31.560][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:31.561][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 20:37:31.563][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 20:37:31.564][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 20:37:31.565][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 20:37:31.567][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 20:37:31.568][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 20:37:31.569][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 20:37:31.571][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 20:37:31.572][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 20:37:31.574][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 20:37:31.575][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 20:37:31.577][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 20:37:31.583][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 20:37:31.585][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 20:37:31.586][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 20:37:31.588][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 20:37:31.589][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 20:37:31.590][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 20:37:31.591][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 20:37:31.593][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 20:37:31.594][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 20:37:31.595][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 20:37:31.597][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 20:37:31.598][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 20:37:31.599][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 20:37:31.601][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 20:37:31.602][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 20:37:31.603][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 20:37:31.605][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 20:37:31.606][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 20:37:31.607][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 20:37:31.609][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 20:37:31.610][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 20:37:31.612][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 20:37:31.613][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 20:37:31.614][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 20:37:31.616][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 20:37:31.617][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 20:37:31.618][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 20:37:31.619][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 20:37:31.621][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 20:37:31.622][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 20:37:31.624][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 20:37:31.625][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 20:37:31.626][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 20:37:31.628][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 20:37:31.629][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 20:37:31.630][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:31.632][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:31.633][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 20:37:31.635][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 20:37:31.636][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 20:37:31.637][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 20:37:31.638][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 20:37:31.640][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 20:37:31.641][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 20:37:31.642][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 20:37:31.644][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 20:37:31.645][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 20:37:31.647][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 20:37:31.648][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 20:37:31.649][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 20:37:31.650][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 20:37:31.652][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 20:37:31.657][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 20:37:31.659][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:31.662][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:31.663][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.665][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.666][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[2024-05-17 20:37:31.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.687][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[2024-05-17 20:37:31.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.746][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[2024-05-17 20:37:31.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:31.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:31.772][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:31.781][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-17 20:37:31.783][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.785][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.786][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.787][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:31.788][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.788][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.789][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.790][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-17 20:37:31.791][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-17 20:37:31.792][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:31.793][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.794][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-17 20:37:31.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-17 20:37:31.796][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-17 20:37:31.797][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:31.798][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:31.798][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:31.798][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:31.799][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-17 20:37:31.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:31.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:31.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:31.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:31.806][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:31.806][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-17 20:37:31.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:31.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:31.808][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:31.809][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-17 20:37:31.809][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-17 20:37:31.815][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:31.817][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:31.823][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-17 20:37:31.825][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:31.826][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:31.828][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:31.853][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-17 20:37:31.854][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-17 20:37:31.858][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-17 20:37:31.863][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-17 20:37:31.868][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:31.869][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:31.870][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-17 20:37:31.871][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-17 20:37:31.881][biodb::testThat]
biodb.INFO [2024-05-17 20:37:31.882][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-17 20:37:31.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:31.884][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:31.888][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-17 20:37:31.890][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:31.894][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:31.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:31.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:31.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:31.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:31.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:31.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:31.925][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.TRACE[2024-05-17 20:37:31.936][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:31.937][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:31.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:31.939][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:31.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:31.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:31.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:31.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:31.957][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:31.959][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:31.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:31.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:31.989][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:31.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:31.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:31.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:31.994][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:31.995][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:31.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:31.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:31.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:31.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.002][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.005][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.012][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.014][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.019][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.022][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.027][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:32.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.031][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:32.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.037][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.038][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.039][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.046][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.054][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:32.055][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.057][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:32.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.063][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.064][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.067][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:32.161][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-17 20:37:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:32.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:32.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.216][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:32.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:32.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:32.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.329][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.389][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.391][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.417][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.418][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.439][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.447][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.448][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.450][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.475][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.476][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.503][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.505][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.519][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.531][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.532][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.534][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.546][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.555][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.559][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.562][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.563][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.575][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.579][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.583][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.615][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.626][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.652][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.653][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.694][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.697][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.701][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.702][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.705][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.709][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.717][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.724][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.727][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.731][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.732][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.734][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.739][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.740][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.742][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.747][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.750][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.755][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.756][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.762][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.765][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.770][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.773][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:32.781][biodb::testThat]
biodb.INFO [2024-05-17 20:37:32.782][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-17 20:37:32.783][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:32.784][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:32.798][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-17 20:37:32.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:32.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-17 20:37:32.813][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:32.814][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-17 20:37:32.815][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:32.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:32.846][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:32.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:32.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:32.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:32.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:32.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:32.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:32.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:32.860][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.861][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.863][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.884][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:32.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.892][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:32.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:32.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.903][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:32.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:32.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.908][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.909][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.911][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.916][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.917][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.919][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:32.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.924][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:32.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.928][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:32.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:32.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.932][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.933][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.936][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:32.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.941][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.944][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:32.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:32.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.949][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:32.950][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.957][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.958][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:32.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:32.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:32.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:32.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:33.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:33.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:33.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:33.006][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-17 20:37:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-17 20:37:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-17 20:37:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-17 20:37:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-17 20:37:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-17 20:37:33.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-17 20:37:33.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:33.027][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.028][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-17 20:37:33.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.030][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:33.033][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.034][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.036][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:33.037][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-17 20:37:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:33.081][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-17 20:37:33.085][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-17 20:37:33.105][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:33.120][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-17 20:37:33.122][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:33.124][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-17 20:37:33.145][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[2024-05-17 20:37:33.149][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:33.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:33.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:33.153][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:33.156][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-17 20:37:33.170][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:33.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:33.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.176][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.177][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.180][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:33.185][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.186][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-17 20:37:33.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.189][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:33.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:33.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:33.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:33.318][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[2024-05-17 20:37:33.321][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:33.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:33.324][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:33.326][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-17 20:37:33.341][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.342][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-17 20:37:33.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.345][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:33.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:33.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:33.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:33.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.389][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:33.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:33.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:33.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:33.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:33.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:33.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:33.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:33.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.436][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:33.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:33.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.452][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 20:37:33.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 20:37:33.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:33.459][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:33.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 20:37:33.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:33.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:33.469][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.470][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-17 20:37:33.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.472][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.479][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.481][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-17 20:37:33.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.482][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.495][biodb::testThat]
biodb.INFO [2024-05-17 20:37:33.497][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-17 20:37:33.498][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:33.499][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:33.503][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-17 20:37:34.293][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-17 20:37:35.664][biodb::testThat]
biodb.INFO [2024-05-17 20:37:35.665][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-17 20:37:35.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:35.667][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:36.172][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[2024-05-17 20:37:36.662][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:36.664][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:36.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.666][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:36.669][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:36.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.671][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:36.673][biodb::testThat]
biodb.INFO [2024-05-17 20:37:36.674][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-17 20:37:36.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:36.676][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:36.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:36.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:36.840][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[2024-05-17 20:37:36.844][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:36.846][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:36.847][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:36.849][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:36.915][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[2024-05-17 20:37:36.918][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:36.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:36.921][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:36.922][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-17 20:37:36.936][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 20:37:36.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 20:37:36.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:36.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:36.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:36.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:36.974][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[2024-05-17 20:37:36.978][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:36.980][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-17 20:37:36.981][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:36.983][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-17 20:37:36.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:36.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:37.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:37.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:37.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:37.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:37.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:37.009][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-17 20:37:37.055][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:37.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-17 20:37:37.059][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:37.060][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:37.061][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:37.062][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:37.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:37.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:37.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:37.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:37.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:37.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:37.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:37.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:37.075][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[2024-05-17 20:37:37.077][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-17 20:37:37.079][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:37.080][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:37.081][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-17 20:37:37.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-17 20:37:38.001][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:38.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-17 20:37:38.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-17 20:37:38.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-17 20:37:38.022][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:38.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:38.025][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:38.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:38.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:38.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:38.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:38.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:38.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:38.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:38.038][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.041][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.046][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:38.048][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:38.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:38.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:38.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.055][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:38.056][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:38.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.058][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:38.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:38.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.063][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:38.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:38.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:38.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:38.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:38.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:38.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.082][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:38.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:38.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.087][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:38.088][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:38.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.090][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.091][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:38.092][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.094][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.095][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:38.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:38.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:38.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.102][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:38.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:38.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.107][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:38.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:38.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.110][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:38.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:38.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.115][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:38.116][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:38.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.119][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:38.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:38.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.123][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:38.124][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:38.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.127][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:38.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:38.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:38.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:38.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:38.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:38.168][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-05-17 20:37:38.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:38.189][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[2024-05-17 20:37:38.192][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:38.194][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-17 20:37:38.195][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:38.196][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-17 20:37:38.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:38.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:38.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:38.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:38.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:38.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:38.219][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:38.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:38.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:38.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:38.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:38.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:38.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:38.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:38.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:38.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:38.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:38.246][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[2024-05-17 20:37:38.247][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-17 20:37:38.248][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:38.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-17 20:37:38.250][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:38.251][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:38.252][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:38.253][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:38.254][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:38.255][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:38.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:38.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:38.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:38.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:38.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:38.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:38.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:38.278][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-17 20:37:38.293][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:38.294][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:38.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-17 20:37:38.756][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-17 20:37:39.483][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:39.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-17 20:37:39.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-17 20:37:39.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-17 20:37:39.494][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:39.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:39.497][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:39.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:39.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:39.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:39.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:39.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:39.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:39.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:39.512][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.515][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.520][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:39.521][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:39.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.523][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.524][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:39.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:39.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.529][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:39.530][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:39.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.532][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:39.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.537][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:39.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:39.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.540][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:39.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:39.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:39.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.554][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:39.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:39.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.558][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:39.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:39.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:39.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:39.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:39.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.577][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:39.583][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:39.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:39.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:39.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.593][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:39.594][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:39.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.597][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:39.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:39.602][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:39.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.604][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:39.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:39.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:39.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:39.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:39.648][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-05-17 20:37:39.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:39.677][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[2024-05-17 20:37:39.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:39.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:39.683][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:39.685][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:39.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:39.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:39.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:39.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:39.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:39.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:39.696][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:39.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:39.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:39.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:39.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:39.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:39.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:39.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:39.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:39.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:39.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:39.719][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-17 20:37:39.720][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:39.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-17 20:37:39.723][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:39.724][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:39.725][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:39.726][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:39.727][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:39.728][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:39.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:39.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:39.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:39.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:39.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:39.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:39.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:39.741][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-17 20:37:39.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:39.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:39.746][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-17 20:37:40.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-17 20:37:40.998][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:41.007][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-17 20:37:41.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-17 20:37:41.025][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-17 20:37:41.104][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:41.106][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:41.108][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:41.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:41.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:41.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:41.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:41.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:41.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:41.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:41.132][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.133][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.136][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.143][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:41.144][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:41.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.149][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:41.150][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:41.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.153][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.155][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:41.156][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:41.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.158][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.160][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:41.161][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:41.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.165][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:41.167][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:41.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.171][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:41.172][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.176][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:41.177][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:41.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.180][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.181][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:41.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:41.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.185][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.192][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:41.193][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:41.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.197][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.202][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:41.204][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:41.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.206][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:41.258][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-05-17 20:37:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:41.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:41.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:41.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:41.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:41.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:41.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:41.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:41.300][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-17 20:37:41.301][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:41.303][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-17 20:37:41.305][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:41.306][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:41.307][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:41.309][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:41.310][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:41.311][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:41.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:41.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:41.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:41.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:41.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:41.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:41.325][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.DEBUG[2024-05-17 20:37:41.327][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-17 20:37:41.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:41.331][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:41.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-17 20:37:41.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-17 20:37:42.283][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:42.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-17 20:37:42.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-17 20:37:42.297][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-17 20:37:42.299][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:42.301][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:42.303][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:42.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:42.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:42.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:42.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:42.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:42.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:42.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:42.323][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.324][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.326][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.331][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:42.332][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:42.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.335][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:42.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:42.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.338][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:42.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:42.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.342][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:42.344][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:42.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.346][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:42.348][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:42.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.350][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.351][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:42.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:42.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:42.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.358][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.359][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:42.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:42.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.362][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.367][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:42.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:42.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:42.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:42.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.375][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:42.376][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:42.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:42.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:42.417][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-05-17 20:37:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:42.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:42.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:42.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:42.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:42.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:42.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:42.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:42.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:42.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:42.447][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-17 20:37:42.448][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:42.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-17 20:37:42.451][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:42.452][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:42.453][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:42.454][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:42.455][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:42.456][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:42.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:42.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:42.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:42.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:42.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:42.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:42.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:42.478][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-17 20:37:42.481][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:42.482][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:42.484][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-17 20:37:42.936][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-17 20:37:43.410][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:43.413][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-17 20:37:43.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-17 20:37:43.422][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-17 20:37:43.424][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:43.426][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:43.428][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:43.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:43.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:43.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:43.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:43.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:43.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:43.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:43.468][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.470][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.472][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.479][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:43.480][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:43.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.483][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:43.485][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:43.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.487][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:43.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:43.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.491][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.493][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:43.494][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:43.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.496][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:43.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:43.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.500][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.502][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:43.503][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.506][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:43.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:43.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.509][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.510][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:43.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:43.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.513][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:43.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:43.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.520][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:43.521][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:43.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.523][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.529][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:43.530][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:43.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.532][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:43.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:43.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:43.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:43.576][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-05-17 20:37:43.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:43.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:43.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:43.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:43.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:43.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:43.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:43.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:43.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:43.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:43.627][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-17 20:37:43.634][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:43.636][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-17 20:37:43.637][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:43.638][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:43.640][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:43.641][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:43.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:43.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:43.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:43.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:43.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:43.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:43.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:43.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:43.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:43.658][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-17 20:37:43.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:43.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:43.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-17 20:37:44.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-17 20:37:44.585][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:44.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-17 20:37:44.597][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-17 20:37:44.602][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-17 20:37:44.605][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:44.607][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:44.610][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:44.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:44.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:44.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:44.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:44.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:44.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:44.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:44.633][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.635][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.639][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.644][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:44.645][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:44.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.647][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:44.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:44.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.652][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:44.653][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:44.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:44.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.661][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:44.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:44.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:44.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:44.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.670][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:44.672][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:44.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:44.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:44.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.679][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:44.681][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:44.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.683][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:44.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.688][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:44.690][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.693][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:44.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:44.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:44.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.700][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:44.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:44.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.706][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:44.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:44.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.709][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:44.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:44.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:44.717][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:44.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.719][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:44.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:44.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:44.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.729][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:44.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:44.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:44.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:44.792][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-05-17 20:37:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:44.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:44.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:44.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:44.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:44.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:44.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:44.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:44.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:44.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:44.820][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[2024-05-17 20:37:44.822][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-17 20:37:44.823][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:44.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-17 20:37:44.827][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:44.828][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:44.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:44.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:44.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:44.833][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:44.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:44.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:44.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:44.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:44.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:44.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:44.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:44.849][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-17 20:37:44.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:44.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:44.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-17 20:37:45.319][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-17 20:37:45.811][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:45.814][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-17 20:37:45.819][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-17 20:37:45.822][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-17 20:37:45.824][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:45.825][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:45.826][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:45.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:45.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:45.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:45.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:45.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:45.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:45.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:45.842][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.845][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.850][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:45.851][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:45.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.853][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.855][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:45.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:45.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.859][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:45.860][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:45.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:45.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:45.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.868][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:45.869][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:45.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:45.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:45.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.876][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:45.877][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:45.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:45.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:45.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:45.885][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:45.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.889][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:45.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:45.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.893][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:45.894][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.896][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.897][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:45.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.901][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:45.902][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:45.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:45.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.910][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:45.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:45.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:45.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:45.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.918][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:45.919][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:45.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.938][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:45.939][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:45.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.941][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.943][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:45.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:45.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:45.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:45.989][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-17 20:37:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:45.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:45.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:45.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:46.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:46.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:46.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:46.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:46.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:46.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:46.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:46.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:46.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:46.025][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-17 20:37:46.027][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:46.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-17 20:37:46.034][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:46.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:46.037][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:46.039][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:46.040][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:46.042][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:46.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:46.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:46.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:46.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:46.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:46.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:46.070][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[2024-05-17 20:37:46.072][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-17 20:37:46.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:46.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:46.078][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-17 20:37:46.531][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-17 20:37:46.990][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:46.993][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-17 20:37:46.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-17 20:37:47.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-17 20:37:47.002][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:47.004][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:47.005][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:47.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:47.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:47.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:47.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:47.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:47.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:47.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:47.021][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.025][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.031][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:47.032][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:47.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.034][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:47.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.041][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:47.042][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:47.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.044][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.046][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:47.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:47.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.050][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:47.052][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:47.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.054][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:47.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:47.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.060][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:47.061][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:47.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.063][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:47.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:47.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:47.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.093][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:47.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.099][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:47.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:47.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:47.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.108][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:47.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:47.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.114][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:47.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:47.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.117][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:47.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:47.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.123][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:47.124][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:47.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.128][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:47.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:47.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.132][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:47.133][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:47.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.135][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:47.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:47.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:47.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:47.182][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-17 20:37:47.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:47.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:47.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:47.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:47.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:47.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:47.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:47.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:47.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:47.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:47.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:47.207][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-17 20:37:47.208][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:47.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-17 20:37:47.211][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:47.212][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:47.213][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:47.214][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:47.215][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:47.216][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:47.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:47.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:47.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:47.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:47.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:47.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:47.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:47.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-17 20:37:47.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:47.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:47.234][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-17 20:37:47.683][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-17 20:37:48.177][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:48.181][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-17 20:37:48.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-17 20:37:48.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-17 20:37:48.198][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:48.201][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:48.203][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:48.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:48.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:48.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:48.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:48.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:48.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:48.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:48.230][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.232][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.235][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.253][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:48.254][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:48.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:48.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:48.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.263][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:48.264][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:48.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.266][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:48.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:48.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.271][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:48.272][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:48.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.274][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:48.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:48.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.279][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:48.280][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:48.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:48.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:48.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.287][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:48.288][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:48.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.291][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:48.292][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.295][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:48.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.299][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:48.300][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:48.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:48.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:48.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:48.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:48.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:48.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:48.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.315][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:48.316][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:48.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.317][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:48.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:48.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:48.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:48.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.325][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.326][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:48.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:48.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:48.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:48.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:48.369][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-05-17 20:37:48.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:48.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:48.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:48.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:48.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:48.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:48.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:48.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:48.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:48.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:48.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:48.391][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-17 20:37:48.392][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:48.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-17 20:37:48.395][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:48.396][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:48.397][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:48.398][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:48.399][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:48.400][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:48.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:48.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:48.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:48.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:48.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:48.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:48.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:48.413][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-17 20:37:48.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:48.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:48.418][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-17 20:37:48.874][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-17 20:37:49.360][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:49.374][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-17 20:37:49.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-17 20:37:49.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-17 20:37:49.398][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:49.402][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:49.405][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:49.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:49.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:49.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:49.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:49.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:49.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:49.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:49.432][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.437][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.444][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:49.445][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:49.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.447][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.449][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:49.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:49.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.453][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:49.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:49.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.456][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:49.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:49.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.462][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:49.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:49.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:49.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:49.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.471][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:49.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:49.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.475][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.480][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:49.481][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:49.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.483][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.485][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:49.486][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.488][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.489][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.494][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:49.495][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:49.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:49.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.503][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:49.504][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:49.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:49.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.512][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:49.513][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:49.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.515][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.517][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:49.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:49.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.521][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:49.522][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:49.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:49.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:49.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:49.572][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-17 20:37:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:49.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:49.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:49.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:49.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:49.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:49.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:49.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:49.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:49.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:49.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:49.613][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-17 20:37:49.614][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:49.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-17 20:37:49.617][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 20:37:49.618][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 20:37:49.619][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:49.620][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:49.621][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 20:37:49.622][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 20:37:49.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:49.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:49.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:49.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:49.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:49.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:49.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:49.639][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-17 20:37:49.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 20:37:49.644][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 20:37:49.646][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-17 20:37:50.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-17 20:37:50.587][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 20:37:50.589][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-17 20:37:50.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-17 20:37:50.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-17 20:37:50.596][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 20:37:50.598][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:50.599][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:50.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:50.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:50.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:50.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:50.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:50.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:50.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:50.612][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.613][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.615][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.620][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:50.621][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:50.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.623][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:50.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:50.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.628][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:50.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:50.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.632][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.637][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:50.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:50.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.640][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:50.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.648][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.653][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:50.654][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:50.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.656][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.657][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:50.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.660][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.661][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:50.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.665][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.666][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.668][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:50.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:50.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.676][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:50.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:50.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.681][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:50.682][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:50.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.684][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.685][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:50.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:50.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.689][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:50.690][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:50.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.693][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:50.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:50.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:50.776][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-17 20:37:50.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:50.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:50.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:50.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:50.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:50.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:50.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:50.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:50.800][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-17 20:37:50.801][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:50.803][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-17 20:37:50.805][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:50.806][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2024-05-17 20:37:50.807][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:50.809][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:50.810][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:50.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:50.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:50.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:50.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:50.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:50.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:50.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:50.824][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.827][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.832][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:50.833][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:50.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.837][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:50.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:50.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.841][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:50.842][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:50.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.844][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.845][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:50.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:50.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.849][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:50.850][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:50.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:50.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:50.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.858][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.859][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.861][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:50.867][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:50.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.869][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.871][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:50.872][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.873][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:50.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.879][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.882][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.887][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:50.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:50.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.890][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.896][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:50.897][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:50.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.899][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.904][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:50.905][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:50.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.907][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:50.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:50.959][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-17 20:37:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:50.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:50.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:50.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:50.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:50.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:50.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:50.981][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.DEBUG[2024-05-17 20:37:50.983][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-17 20:37:50.984][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:50.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-17 20:37:50.987][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:50.988][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2024-05-17 20:37:50.989][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:50.991][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:50.992][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:50.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:50.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:50.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.005][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.008][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.014][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.015][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.016][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.022][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.025][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.030][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.031][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.035][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.036][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.039][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.040][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.042][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.043][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.044][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.046][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.051][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.052][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.054][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.059][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.060][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.068][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.069][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.071][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.072][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.076][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.077][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.079][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.126][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-17 20:37:51.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.149][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[2024-05-17 20:37:51.150][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-17 20:37:51.151][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:51.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-17 20:37:51.154][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:51.156][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-05-17 20:37:51.157][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:51.158][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:51.160][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:51.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.173][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.176][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.182][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.183][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.184][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.190][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.193][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.198][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.199][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.202][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.203][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.205][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.206][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.207][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.209][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.211][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.212][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.214][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.219][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.220][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.222][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.227][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.235][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.236][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.238][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.239][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.243][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.246][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.286][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-05-17 20:37:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:51.315][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-17 20:37:51.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:51.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-17 20:37:51.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:51.321][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-05-17 20:37:51.322][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:51.323][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:51.324][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:51.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.338][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.339][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.346][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.347][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.348][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.350][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.354][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.356][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.362][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.363][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.364][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.370][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.372][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.378][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.380][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.382][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.383][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.386][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.390][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.391][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.393][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.398][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.399][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.406][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.407][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.409][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.410][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.414][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.417][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.461][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-05-17 20:37:51.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:51.491][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-17 20:37:51.492][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:51.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-17 20:37:51.495][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:51.496][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2024-05-17 20:37:51.497][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:51.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:51.500][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:51.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.521][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.522][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.525][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.530][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.531][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.532][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.538][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.539][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.541][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.555][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.556][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.558][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.559][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.560][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.562][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.564][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.577][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.578][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.585][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.594][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.595][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.640][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-05-17 20:37:51.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:51.669][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-17 20:37:51.670][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:51.671][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-17 20:37:51.673][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:51.674][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2024-05-17 20:37:51.675][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:51.677][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:51.678][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:51.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.690][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.691][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.693][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.698][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.699][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.701][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.706][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.709][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.714][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.715][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.722][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.723][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.724][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.730][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.731][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.734][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.735][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.737][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.738][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.742][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.743][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.745][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.750][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.753][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.758][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.759][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.761][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.762][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.766][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.767][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.812][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-05-17 20:37:51.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:51.841][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-17 20:37:51.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:51.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-17 20:37:51.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:51.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2024-05-17 20:37:51.848][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:51.849][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:51.850][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:51.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:51.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:51.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:51.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:51.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:51.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:51.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:51.863][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.871][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.872][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:51.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:51.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.879][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.880][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.882][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:51.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:51.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:51.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:51.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.894][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.895][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.897][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:51.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.902][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:51.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.905][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.906][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.907][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.909][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:51.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.915][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.916][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.918][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.923][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.924][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.926][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:51.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:51.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.931][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.932][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.934][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.935][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:51.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.939][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.940][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.941][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.943][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:51.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:51.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:51.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:51.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:51.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:51.985][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-05-17 20:37:51.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:51.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:51.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:52.012][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-17 20:37:52.013][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:52.015][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-17 20:37:52.016][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:52.018][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2024-05-17 20:37:52.019][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:52.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:52.021][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:52.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:52.034][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.035][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.042][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.043][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.045][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.050][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.053][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.059][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.067][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.068][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.074][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.075][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.077][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.078][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.079][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.081][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.094][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.097][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.102][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.103][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.106][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.110][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.111][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.113][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.166][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-05-17 20:37:52.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.226][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[2024-05-17 20:37:52.227][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-17 20:37:52.228][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:52.231][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-17 20:37:52.232][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:52.234][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2024-05-17 20:37:52.236][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:52.237][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:52.238][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:52.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:52.253][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.262][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.263][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.266][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.270][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.273][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.287][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.288][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.297][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.298][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.302][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.307][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.321][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.329][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.331][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.334][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.339][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.387][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-05-17 20:37:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.413][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[2024-05-17 20:37:52.414][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-17 20:37:52.415][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:52.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-17 20:37:52.418][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:52.420][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-05-17 20:37:52.421][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:52.422][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:52.423][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:52.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:52.435][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.438][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.443][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.444][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.446][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.447][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:52.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:52.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.451][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.452][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.454][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:52.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:52.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:52.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.467][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.468][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.469][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:52.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.474][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.475][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:52.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.478][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.481][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.482][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:52.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.489][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:52.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.494][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.502][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.503][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.510][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.513][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:52.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:52.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.558][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-05-17 20:37:52.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.595][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[2024-05-17 20:37:52.598][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:52.600][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:52.601][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:52.603][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:52.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.615][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.636][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.666][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.TRACE[2024-05-17 20:37:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.696][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.725][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.752][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.774][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.795][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.816][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.836][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.857][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.878][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.899][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[2024-05-17 20:37:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.924][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.944][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.964][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:52.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:52.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:52.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:52.985][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:52.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:52.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:52.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:52.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:52.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:52.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:52.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.005][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.026][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.046][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[2024-05-17 20:37:53.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.120][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[2024-05-17 20:37:53.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:53.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-05-17 20:37:53.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.127][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-05-17 20:37:53.130][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[2024-05-17 20:37:53.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:53.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-05-17 20:37:53.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.136][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-05-17 20:37:53.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:53.149][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-17 20:37:53.149][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:53.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-17 20:37:53.152][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.154][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-05-17 20:37:53.155][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:53.156][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:53.157][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:53.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:53.169][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.172][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.177][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:53.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:53.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.180][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.181][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:53.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.185][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:53.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:53.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.188][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.189][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:53.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:53.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:53.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:53.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:53.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:53.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.201][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.204][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.209][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.209][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.211][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.212][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.216][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:53.217][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.219][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.220][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:53.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.224][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.225][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.227][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.237][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:53.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:53.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.240][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:53.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:53.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.245][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:53.246][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:53.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.248][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.249][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:53.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:53.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.253][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:53.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:53.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.257][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:53.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:53.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.298][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-05-17 20:37:53.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.319][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.TRACE[2024-05-17 20:37:53.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:53.342][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-17 20:37:53.343][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:53.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-17 20:37:53.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.347][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-05-17 20:37:53.348][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:53.349][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:53.350][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:53.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:53.362][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.365][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.370][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:53.371][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:53.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.373][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:53.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:53.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.378][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:53.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:53.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.381][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:53.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:53.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:53.387][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:53.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.388][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:53.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:53.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.393][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.394][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:53.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.406][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.407][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:53.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.409][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.410][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:53.411][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:53.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:53.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.418][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.419][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.421][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.426][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:53.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:53.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.428][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.434][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:53.435][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:53.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.436][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.437][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:53.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:53.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.441][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:53.442][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:53.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.444][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.445][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:53.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:53.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:53.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:53.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.486][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-05-17 20:37:53.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.513][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[2024-05-17 20:37:53.516][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:53.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:53.518][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.520][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:53.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.531][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[2024-05-17 20:37:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.551][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[2024-05-17 20:37:53.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.585][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.613][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[2024-05-17 20:37:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.642][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.663][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.684][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.705][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.730][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.751][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.772][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.792][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.812][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.832][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.853][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.875][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.900][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.TRACE[2024-05-17 20:37:53.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.920][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.940][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:53.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:53.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:53.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:53.961][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:53.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:53.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:53.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:53.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:53.988][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[2024-05-17 20:37:53.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:53.992][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-17 20:37:53.993][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:53.994][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-17 20:37:53.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:53.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:53.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.005][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.025][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.059][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.088][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.116][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.137][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.158][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.TRACE[2024-05-17 20:37:54.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.187][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.210][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.TRACE[2024-05-17 20:37:54.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.248][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.270][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.292][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.TRACE[2024-05-17 20:37:54.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.314][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.336][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.TRACE[2024-05-17 20:37:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.358][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.379][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[2024-05-17 20:37:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.399][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.427][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.448][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.TRACE[2024-05-17 20:37:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.468][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.492][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:54.503][biodb::testThat]
biodb.INFO [2024-05-17 20:37:54.504][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-17 20:37:54.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:54.505][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:54.509][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 20:37:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 20:37:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.540][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[2024-05-17 20:37:54.543][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[2024-05-17 20:37:54.547][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:54.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-17 20:37:54.549][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:54.551][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-17 20:37:54.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.562][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.581][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[2024-05-17 20:37:54.584][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:54.586][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-17 20:37:54.587][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:54.588][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-17 20:37:54.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.599][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.620][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.632][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:54.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.642][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.652][private$selectFields]
biodb.TRACE[2024-05-17 20:37:54.652][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:54.653][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:54.654][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.655][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.658][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.659][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.660][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.662][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.667][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.668][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:54.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.689][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-17 20:37:54.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:54.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.707][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.708][private$selectFields]
biodb.TRACE[2024-05-17 20:37:54.709][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:54.710][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:54.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.712][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.714][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.718][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.719][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.720][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.721][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.722][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.723][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.724][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:54.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.742][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:54.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.752][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.762][private$selectFields]
biodb.TRACE[2024-05-17 20:37:54.763][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:54.764][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:54.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.767][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.773][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:54.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.777][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.781][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:54.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:54.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.804][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-17 20:37:54.805][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:54.806][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:54.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:54.907][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[2024-05-17 20:37:54.910][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:54.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-17 20:37:54.913][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:54.915][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-17 20:37:54.923][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[2024-05-17 20:37:54.926][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:54.928][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-17 20:37:54.929][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:54.930][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-17 20:37:54.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.941][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.963][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:54.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:54.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:54.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:54.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:54.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:54.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:54.984][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:54.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:54.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:54.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:54.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.020][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:55.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.053][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.062][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.063][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.064][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.065][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.068][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.069][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.070][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.071][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.073][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.080][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.081][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.082][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.085][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.086][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.099][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-17 20:37:55.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:55.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.150][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.151][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.152][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.156][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.158][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.160][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.161][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.171][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.172][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.175][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.176][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.189][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:55.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.200][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.208][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.209][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.210][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.211][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.212][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.221][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.223][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.226][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.244][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-17 20:37:55.245][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:55.246][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:55.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:55.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:55.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:55.260][biodb::testThat]
biodb.INFO [2024-05-17 20:37:55.261][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-17 20:37:55.262][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:55.263][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:55.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 20:37:55.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 20:37:55.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.295][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[2024-05-17 20:37:55.297][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[2024-05-17 20:37:55.300][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-17 20:37:55.303][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.304][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-17 20:37:55.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.315][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.TRACE[2024-05-17 20:37:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.328][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[2024-05-17 20:37:55.331][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-17 20:37:55.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.334][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-17 20:37:55.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.345][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.366][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.379][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:55.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.389][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.403][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.404][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.405][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.406][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.409][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.410][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.411][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.412][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.414][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.416][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.420][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.433][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-17 20:37:55.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:55.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.451][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.452][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.453][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.454][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.455][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.456][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.457][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.458][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.463][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.464][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.465][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.466][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.467][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.468][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.481][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:55.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.490][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.500][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.501][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.502][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.512][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.515][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.529][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-17 20:37:55.530][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:55.531][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.570][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[2024-05-17 20:37:55.573][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[2024-05-17 20:37:55.576][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-17 20:37:55.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.579][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-17 20:37:55.582][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[2024-05-17 20:37:55.585][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.586][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-17 20:37:55.587][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.589][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-17 20:37:55.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.600][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.TRACE[2024-05-17 20:37:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.622][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.TRACE[2024-05-17 20:37:55.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.643][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.655][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:55.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.665][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[2024-05-17 20:37:55.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.674][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.675][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.675][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.676][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.677][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.678][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.681][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.682][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.683][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.686][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.687][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.690][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.691][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.704][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-17 20:37:55.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:55.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.728][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.730][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.731][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.733][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.734][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.735][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.740][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.741][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.742][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.745][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.746][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:55.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.768][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.778][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.779][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.779][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.780][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.782][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.784][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.785][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.786][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.788][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.790][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.791][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.792][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.794][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.807][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-17 20:37:55.808][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:55.809][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:55.818][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:55.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:55.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:55.825][biodb::testThat]
biodb.INFO [2024-05-17 20:37:55.826][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-17 20:37:55.827][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:55.827][biodb::testThat]
biodb.TRACE[2024-05-17 20:37:55.830][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 20:37:55.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 20:37:55.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:55.865][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[2024-05-17 20:37:55.868][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-17 20:37:55.871][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.872][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-17 20:37:55.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.883][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.902][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[2024-05-17 20:37:55.906][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:55.907][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-17 20:37:55.908][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:55.909][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-17 20:37:55.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.920][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.941][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:55.954][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:55.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:55.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:55.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:55.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:55.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:55.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:55.964][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.973][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.973][private$selectFields]
biodb.TRACE[2024-05-17 20:37:55.974][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:55.975][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:55.976][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.977][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.978][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.980][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.981][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.982][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.985][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:55.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.987][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.989][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.990][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:55.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:55.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:55.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.002][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-17 20:37:56.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:56.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.022][private$selectFields]
biodb.TRACE[2024-05-17 20:37:56.023][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:56.023][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:56.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.032][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.034][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.036][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.038][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:56.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.067][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:56.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.075][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.076][private$selectFields]
biodb.TRACE[2024-05-17 20:37:56.077][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:56.078][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:56.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.081][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.083][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.087][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.088][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.092][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.093][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:56.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.106][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-17 20:37:56.107][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:56.107][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:56.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:56.154][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[2024-05-17 20:37:56.157][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:56.158][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-17 20:37:56.160][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:56.161][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-17 20:37:56.164][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[2024-05-17 20:37:56.167][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:56.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-17 20:37:56.170][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:56.171][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-17 20:37:56.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.182][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:56.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.204][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[2024-05-17 20:37:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.230][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.TRACE[2024-05-17 20:37:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.243][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 20:37:56.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.253][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.TRACE[2024-05-17 20:37:56.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.262][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.263][private$selectFields]
biodb.TRACE[2024-05-17 20:37:56.264][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:56.265][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:56.266][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.267][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.268][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.274][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.275][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.276][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.280][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:56.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.293][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-17 20:37:56.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.311][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.312][private$selectFields]
biodb.TRACE[2024-05-17 20:37:56.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:56.313][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:56.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.322][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.323][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.327][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.328][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:56.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.340][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-17 20:37:56.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.350][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:56.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.359][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.359][private$selectFields]
biodb.TRACE[2024-05-17 20:37:56.360][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 20:37:56.361][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 20:37:56.362][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.364][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.366][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.368][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.372][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-17 20:37:56.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.375][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.376][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-17 20:37:56.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.395][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-17 20:37:56.396][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 20:37:56.397][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 20:37:56.413][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 20:37:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:56.420][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.421][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-17 20:37:56.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:56.422][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:56.424][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-17 20:37:56.425][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:56.426][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-17 20:37:56.428][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:56.429][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-05-17 20:37:56.430][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:56.431][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:56.432][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:56.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:56.444][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.447][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.452][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.453][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.454][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.456][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.457][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.458][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.460][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.461][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.464][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.465][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.468][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.470][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.471][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.472][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.474][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.475][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.476][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.479][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.483][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.484][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.486][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.529][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-17 20:37:56.530][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-17 20:37:56.537][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.538][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-17 20:37:56.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:56.540][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:56.554][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-17 20:37:56.555][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-17 20:37:56.556][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-17 20:37:56.558][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-17 20:37:56.559][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-05-17 20:37:56.561][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-05-17 20:37:56.562][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:56.564][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-17 20:37:56.565][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:56.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.575][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.TRACE[2024-05-17 20:37:56.577][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.585][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.586][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.589][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.590][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.591][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.593][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.594][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.597][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.598][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.599][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.601][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.602][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.603][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.604][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.605][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.608][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.611][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.612][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.613][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.615][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.616][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.617][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.619][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.620][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.623][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.659][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:56.661][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.669][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.670][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.671][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.677][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.677][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.679][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.681][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.685][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.685][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.687][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.692][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.693][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.695][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.700][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.701][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.708][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.709][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.716][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.722][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.724][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.729][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.737][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.738][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.740][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.741][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.748][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.749][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:56.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:56.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:56.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:56.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:56.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:56.787][FUN] Functions in observer BiodbConfig: [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[2024-05-17 20:37:56.790][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.798][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.799][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.800][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.802][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:56.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:56.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.805][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.806][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.808][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.813][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.814][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:56.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:56.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.821][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.822][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:56.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.829][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.830][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:56.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.837][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.838][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.839][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.841][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:56.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:56.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.846][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.852][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:56.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:56.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.860][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.861][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.863][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.864][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:56.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:56.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.868][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.869][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.878][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:56.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:56.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:56.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:56.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:56.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:56.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:56.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:56.942][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-17 20:37:56.943][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-17 20:37:56.944][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-05-17 20:37:56.956][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.957][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-17 20:37:56.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:56.959][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.981][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.982][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-17 20:37:56.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:56.984][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.991][biodb::testThat]
biodb.INFO [2024-05-17 20:37:56.992][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-17 20:37:56.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:56.994][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:56.997][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[2024-05-17 20:37:57.000][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.001][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-05-17 20:37:57.002][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.004][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-05-17 20:37:57.014][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:57.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:57.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:57.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:57.018][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:57.019][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:57.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:57.020][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 20:37:57.022][biodb::testThat]
biodb.INFO [2024-05-17 20:37:57.023][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-17 20:37:57.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:57.025][biodb::testThat]
biodb.ERROR[2024-05-17 20:37:57.044][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-17 20:37:57.061][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-17 20:37:57.074][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 20:37:57.076][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-17 20:37:57.077][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-17 20:37:57.078][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 20:37:57.078][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.080][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.082][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.083][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 20:37:57.092][biodb::testContext]
biodb.INFO [2024-05-17 20:37:57.093][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:57.094][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-17 20:37:57.095][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:57.096][biodb::testContext]
biodb.INFO [2024-05-17 20:37:57.098][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:57.100][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:57.103][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:57.104][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 20:37:57.105][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.109][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 20:37:57.110][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.113][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 20:37:57.114][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.118][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 20:37:57.119][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 20:37:57.120][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 20:37:57.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.123][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 20:37:57.124][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 20:37:57.125][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.128][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 20:37:57.129][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 20:37:57.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.132][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[2024-05-17 20:37:57.133][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 20:37:57.133][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 20:37:57.134][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 20:37:57.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.138][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 20:37:57.139][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.142][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 20:37:57.143][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 20:37:57.144][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 20:37:57.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.147][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:57.148][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 20:37:57.149][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 20:37:57.150][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 20:37:57.151][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 20:37:57.152][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 20:37:57.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.155][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 20:37:57.156][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 20:37:57.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.160][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 20:37:57.161][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 20:37:57.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.164][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 20:37:57.165][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 20:37:57.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.168][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 20:37:57.169][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 20:37:57.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.173][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 20:37:57.174][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 20:37:57.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.177][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:57.178][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 20:37:57.182][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 20:37:57.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.184][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[2024-05-17 20:37:57.185][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 20:37:57.186][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 20:37:57.187][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 20:37:57.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.191][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 20:37:57.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.194][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 20:37:57.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:57.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.204][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.205][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.206][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:57.207][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:57.208][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.209][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 20:37:57.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:57.211][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.212][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.213][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:57.213][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:57.213][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:57.213][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:57.213][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:57.214][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:57.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.217][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:57.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.220][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.221][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:57.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:57.223][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.224][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.225][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 20:37:57.227][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.228][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:57.229][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.230][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:57.231][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.232][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.232][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.233][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.234][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:57.235][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:57.236][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.237][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 20:37:57.238][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:57.239][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.240][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.241][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:57.241][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:57.241][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:57.241][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:57.241][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:57.242][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:57.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:57.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.247][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.248][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:57.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:57.251][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.252][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.253][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 20:37:57.254][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.255][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 20:37:57.256][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.257][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:57.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.262][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:57.263][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:57.264][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.265][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 20:37:57.266][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:57.267][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.268][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.268][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:57.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:57.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.276][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:57.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:57.278][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.279][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.280][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 20:37:57.282][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.283][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:57.284][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:57.286][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.287][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.288][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.289][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:57.290][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:57.291][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.292][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 20:37:57.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:57.294][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.295][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.296][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.297][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:57.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:57.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.302][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.303][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:57.305][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:57.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.307][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:57.308][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:57.309][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.318][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[2024-05-17 20:37:57.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.344][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[2024-05-17 20:37:57.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.375][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[2024-05-17 20:37:57.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.379][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.DEBUG[2024-05-17 20:37:57.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.388][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 20:37:57.390][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 20:37:57.391][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 20:37:57.393][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 20:37:57.394][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:57.395][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 20:37:57.397][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:57.398][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:57.399][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 20:37:57.400][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 20:37:57.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:57.403][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 20:37:57.404][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:57.406][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:57.407][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 20:37:57.408][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 20:37:57.409][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 20:37:57.411][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 20:37:57.412][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:57.413][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 20:37:57.415][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 20:37:57.416][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 20:37:57.417][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 20:37:57.418][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 20:37:57.420][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 20:37:57.421][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 20:37:57.422][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 20:37:57.424][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 20:37:57.425][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 20:37:57.426][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 20:37:57.427][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 20:37:57.429][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 20:37:57.430][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 20:37:57.431][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 20:37:57.433][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 20:37:57.434][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 20:37:57.435][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 20:37:57.436][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 20:37:57.438][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 20:37:57.439][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 20:37:57.440][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 20:37:57.442][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 20:37:57.443][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 20:37:57.444][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 20:37:57.446][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 20:37:57.447][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 20:37:57.448][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 20:37:57.450][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 20:37:57.451][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 20:37:57.452][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 20:37:57.454][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 20:37:57.455][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 20:37:57.456][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 20:37:57.458][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 20:37:57.459][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 20:37:57.460][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 20:37:57.461][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 20:37:57.463][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 20:37:57.464][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 20:37:57.465][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 20:37:57.467][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 20:37:57.468][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 20:37:57.469][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 20:37:57.471][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 20:37:57.472][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 20:37:57.473][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 20:37:57.475][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:57.476][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:57.477][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 20:37:57.479][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 20:37:57.480][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 20:37:57.481][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 20:37:57.483][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 20:37:57.484][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 20:37:57.485][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 20:37:57.487][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 20:37:57.488][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 20:37:57.489][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 20:37:57.491][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 20:37:57.492][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 20:37:57.493][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 20:37:57.495][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 20:37:57.496][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 20:37:57.497][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 20:37:57.499][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:57.500][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:57.501][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.502][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.503][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[2024-05-17 20:37:57.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.528][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[2024-05-17 20:37:57.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.541][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[2024-05-17 20:37:57.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.547][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[2024-05-17 20:37:57.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.559][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[2024-05-17 20:37:57.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.564][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[2024-05-17 20:37:57.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.570][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[2024-05-17 20:37:57.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.576][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[2024-05-17 20:37:57.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.582][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[2024-05-17 20:37:57.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.588][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[2024-05-17 20:37:57.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.605][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.DEBUG[2024-05-17 20:37:57.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:57.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.613][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:57.614][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-17 20:37:57.616][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.617][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.618][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.619][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:57.620][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.621][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.622][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.623][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-17 20:37:57.624][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-17 20:37:57.625][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:57.626][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.627][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-17 20:37:57.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-17 20:37:57.629][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-17 20:37:57.630][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:57.631][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:57.631][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:57.631][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:57.632][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-17 20:37:57.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.634][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:57.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:57.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:57.637][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:57.638][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:57.638][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-17 20:37:57.639][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:57.640][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:57.641][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:57.642][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-17 20:37:57.642][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-17 20:37:57.643][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:57.645][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:57.646][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-17 20:37:57.648][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:57.649][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:57.650][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:57.654][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-17 20:37:57.655][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-17 20:37:57.656][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-17 20:37:57.657][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-17 20:37:57.659][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:57.660][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:57.661][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-17 20:37:57.667][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-17 20:37:57.669][biodb::testThat]
biodb.INFO [2024-05-17 20:37:57.670][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-17 20:37:57.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:57.672][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:57.675][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-17 20:37:57.679][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.680][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-17 20:37:57.681][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.683][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-17 20:37:57.686][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[2024-05-17 20:37:57.689][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-17 20:37:57.692][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.693][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-17 20:37:57.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.705][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[2024-05-17 20:37:57.708][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-17 20:37:57.711][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.712][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-17 20:37:57.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.752][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[2024-05-17 20:37:57.755][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-17 20:37:57.757][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.758][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-17 20:37:57.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.771][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[2024-05-17 20:37:57.774][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.775][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-17 20:37:57.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.778][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-17 20:37:57.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.802][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[2024-05-17 20:37:57.805][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-17 20:37:57.807][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.809][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-17 20:37:57.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:57.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:57.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:57.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:57.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:57.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:57.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:57.821][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[2024-05-17 20:37:57.824][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:57.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-17 20:37:57.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:57.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-17 20:37:57.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:58.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.091][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[2024-05-17 20:37:58.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:58.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-05-17 20:37:58.097][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:58.098][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-05-17 20:37:58.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:58.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.109][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 20:37:58.115][biodb::testThat]
biodb.INFO [2024-05-17 20:37:58.116][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-17 20:37:58.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:58.118][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:58.121][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[2024-05-17 20:37:58.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:58.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-05-17 20:37:58.126][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:58.128][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-05-17 20:37:58.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:58.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.138][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[2024-05-17 20:37:58.141][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[2024-05-17 20:37:58.144][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:58.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-05-17 20:37:58.146][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:58.148][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-05-17 20:37:58.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:58.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.157][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 20:37:58.161][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 20:37:58.163][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-17 20:37:58.164][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-17 20:37:58.164][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 20:37:58.165][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.167][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.168][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.169][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 20:37:58.172][biodb::testContext]
biodb.INFO [2024-05-17 20:37:58.173][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:58.174][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-17 20:37:58.175][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:58.176][biodb::testContext]
biodb.INFO [2024-05-17 20:37:58.182][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:58.185][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:58.189][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:58.190][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 20:37:58.192][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.195][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 20:37:58.196][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.199][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[2024-05-17 20:37:58.200][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 20:37:58.201][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.205][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 20:37:58.206][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 20:37:58.207][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.210][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[2024-05-17 20:37:58.211][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 20:37:58.212][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 20:37:58.213][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.217][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 20:37:58.218][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.221][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 20:37:58.222][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 20:37:58.224][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 20:37:58.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.228][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 20:37:58.229][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.234][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 20:37:58.235][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 20:37:58.236][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.240][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:58.241][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 20:37:58.242][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 20:37:58.243][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 20:37:58.244][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 20:37:58.245][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 20:37:58.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.249][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 20:37:58.250][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 20:37:58.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.253][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 20:37:58.254][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 20:37:58.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.257][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[2024-05-17 20:37:58.258][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 20:37:58.259][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.263][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 20:37:58.264][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 20:37:58.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.269][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 20:37:58.270][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 20:37:58.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.274][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:58.275][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 20:37:58.278][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 20:37:58.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.283][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 20:37:58.284][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 20:37:58.285][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 20:37:58.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.290][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 20:37:58.292][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 20:37:58.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.302][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:58.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.306][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 20:37:58.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.308][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.309][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:58.311][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:58.311][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:58.311][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:58.311][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:58.312][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.315][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.318][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.319][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.320][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.321][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.322][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.323][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.324][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 20:37:58.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.327][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:58.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.332][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.334][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.335][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:58.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.337][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.338][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 20:37:58.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.340][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:58.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:58.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:58.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:58.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:58.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.350][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.351][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.352][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.353][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.354][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.355][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 20:37:58.357][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.358][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 20:37:58.359][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.361][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.366][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:58.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.368][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.369][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 20:37:58.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.371][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.372][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.373][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.374][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.381][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.384][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.385][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.386][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 20:37:58.388][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.389][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:58.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.393][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.394][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.396][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.397][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:58.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.399][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.400][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 20:37:58.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.402][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.404][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.412][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.416][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.430][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:58.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.437][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[2024-05-17 20:37:58.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.454][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[2024-05-17 20:37:58.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.472][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[2024-05-17 20:37:58.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.481][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[2024-05-17 20:37:58.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.485][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[2024-05-17 20:37:58.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.503][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[2024-05-17 20:37:58.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.508][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 20:37:58.510][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 20:37:58.511][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 20:37:58.512][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 20:37:58.514][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:58.515][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 20:37:58.516][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:58.518][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:58.519][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 20:37:58.521][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 20:37:58.522][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:58.523][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 20:37:58.524][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:58.526][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:58.527][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 20:37:58.528][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 20:37:58.529][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 20:37:58.531][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 20:37:58.532][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:58.533][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 20:37:58.535][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 20:37:58.536][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 20:37:58.537][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 20:37:58.538][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 20:37:58.540][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 20:37:58.541][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 20:37:58.542][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 20:37:58.543][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 20:37:58.545][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 20:37:58.546][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 20:37:58.547][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 20:37:58.548][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 20:37:58.550][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 20:37:58.551][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 20:37:58.552][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 20:37:58.553][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 20:37:58.555][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 20:37:58.556][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 20:37:58.557][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 20:37:58.559][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 20:37:58.560][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 20:37:58.561][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 20:37:58.563][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 20:37:58.564][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 20:37:58.565][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 20:37:58.567][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 20:37:58.568][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 20:37:58.569][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 20:37:58.570][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 20:37:58.572][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 20:37:58.573][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 20:37:58.574][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 20:37:58.576][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 20:37:58.577][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 20:37:58.578][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 20:37:58.579][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 20:37:58.581][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 20:37:58.582][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 20:37:58.583][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 20:37:58.585][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 20:37:58.586][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 20:37:58.587][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 20:37:58.588][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 20:37:58.590][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 20:37:58.591][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 20:37:58.592][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 20:37:58.594][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:58.595][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:58.596][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 20:37:58.597][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 20:37:58.599][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 20:37:58.600][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 20:37:58.601][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 20:37:58.603][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 20:37:58.604][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 20:37:58.605][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 20:37:58.607][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 20:37:58.608][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 20:37:58.609][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 20:37:58.611][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 20:37:58.612][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 20:37:58.613][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 20:37:58.614][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 20:37:58.616][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 20:37:58.617][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:58.618][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:58.619][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.621][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.622][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[2024-05-17 20:37:58.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.639][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[2024-05-17 20:37:58.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.651][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[2024-05-17 20:37:58.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.709][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[2024-05-17 20:37:58.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.727][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:58.729][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-17 20:37:58.730][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.731][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.732][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.733][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.734][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.735][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.736][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.737][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-17 20:37:58.738][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-17 20:37:58.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.739][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.740][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-17 20:37:58.741][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-17 20:37:58.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-17 20:37:58.743][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.744][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:58.744][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:58.744][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:58.745][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-17 20:37:58.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.748][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.751][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:58.751][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-17 20:37:58.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.754][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.755][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-17 20:37:58.755][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-17 20:37:58.756][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:58.758][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:58.759][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-17 20:37:58.760][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:58.762][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:58.763][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:58.767][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-17 20:37:58.767][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-17 20:37:58.769][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-17 20:37:58.770][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-17 20:37:58.771][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:58.772][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:58.773][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-17 20:37:58.774][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-17 20:37:58.776][biodb::testThat]
biodb.INFO [2024-05-17 20:37:58.777][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-17 20:37:58.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:58.778][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:58.781][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-17 20:37:58.785][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:58.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-17 20:37:58.787][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:58.789][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-17 20:37:58.792][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[2024-05-17 20:37:58.795][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:58.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-17 20:37:58.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:58.799][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-05-17 20:37:58.806][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 20:37:58.807][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-17 20:37:58.808][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-17 20:37:58.809][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 20:37:58.810][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:58.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:58.812][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:58.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:58.813][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.814][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 20:37:58.818][biodb::testContext]
biodb.INFO [2024-05-17 20:37:58.819][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:58.819][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-17 20:37:58.820][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 20:37:58.821][biodb::testContext]
biodb.INFO [2024-05-17 20:37:58.823][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:58.825][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:58.828][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:58.829][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 20:37:58.830][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.834][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 20:37:58.835][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.837][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[2024-05-17 20:37:58.838][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 20:37:58.839][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.843][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 20:37:58.844][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 20:37:58.845][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.848][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 20:37:58.849][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 20:37:58.850][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.853][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 20:37:58.854][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.858][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 20:37:58.859][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 20:37:58.860][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 20:37:58.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.863][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 20:37:58.864][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.868][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 20:37:58.869][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 20:37:58.870][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 20:37:58.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.873][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:58.874][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 20:37:58.875][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 20:37:58.876][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 20:37:58.877][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 20:37:58.878][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 20:37:58.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.881][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 20:37:58.882][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 20:37:58.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.885][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 20:37:58.886][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 20:37:58.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.890][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 20:37:58.891][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 20:37:58.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.894][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 20:37:58.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 20:37:58.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.898][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.DEBUG[2024-05-17 20:37:58.898][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 20:37:58.899][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 20:37:58.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.903][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 20:37:58.904][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 20:37:58.907][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 20:37:58.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.909][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[2024-05-17 20:37:58.910][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 20:37:58.911][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 20:37:58.912][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 20:37:58.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:58.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:58.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:58.916][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 20:37:58.917][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.918][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 20:37:58.919][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.920][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.921][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.922][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.925][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:58.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.927][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.928][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 20:37:58.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.929][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.930][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.931][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:58.931][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:58.931][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:58.931][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:58.931][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:58.932][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.935][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.938][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.941][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.942][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.943][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 20:37:58.945][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.946][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:58.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.950][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:58.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.955][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 20:37:58.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.957][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:58.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:58.959][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:58.959][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 20:37:58.959][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 20:37:58.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.965][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.966][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.967][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.968][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.969][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.970][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 20:37:58.972][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.973][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 20:37:58.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:58.976][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.980][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 20:37:58.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:58.982][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.982][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 20:37:58.983][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:58.984][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.985][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:58.986][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.987][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:58.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:58.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:58.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:58.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:58.993][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:58.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:58.996][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:58.997][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:58.998][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 20:37:58.999][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.000][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 20:37:59.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:59.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:59.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.007][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 20:37:59.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:59.009][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:59.010][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 20:37:59.011][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:59.012][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:59.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.014][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:59.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 20:37:59.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:59.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:59.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:59.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:59.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:59.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.026][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:59.027][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:59.028][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:59.029][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:59.029][self$setPropertyValue]
biodb.DEBUG[2024-05-17 20:37:59.031][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:59.031][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.045][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[2024-05-17 20:37:59.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.049][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[2024-05-17 20:37:59.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.065][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[2024-05-17 20:37:59.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.069][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[2024-05-17 20:37:59.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.077][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[2024-05-17 20:37:59.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.081][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[2024-05-17 20:37:59.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.102][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 20:37:59.104][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 20:37:59.105][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 20:37:59.106][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 20:37:59.107][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:59.109][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 20:37:59.110][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:59.111][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:59.113][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 20:37:59.114][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 20:37:59.115][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:59.116][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 20:37:59.118][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 20:37:59.119][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 20:37:59.120][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 20:37:59.121][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 20:37:59.123][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 20:37:59.124][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 20:37:59.125][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:59.127][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 20:37:59.128][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 20:37:59.129][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 20:37:59.130][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 20:37:59.132][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 20:37:59.133][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 20:37:59.134][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 20:37:59.135][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 20:37:59.137][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 20:37:59.138][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 20:37:59.139][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 20:37:59.141][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 20:37:59.142][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 20:37:59.143][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 20:37:59.145][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 20:37:59.146][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 20:37:59.147][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 20:37:59.148][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 20:37:59.150][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 20:37:59.151][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 20:37:59.152][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 20:37:59.153][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 20:37:59.155][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 20:37:59.156][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 20:37:59.157][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 20:37:59.159][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 20:37:59.160][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 20:37:59.161][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 20:37:59.163][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 20:37:59.164][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 20:37:59.165][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 20:37:59.166][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 20:37:59.168][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 20:37:59.169][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 20:37:59.170][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 20:37:59.171][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 20:37:59.173][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 20:37:59.174][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 20:37:59.175][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 20:37:59.177][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 20:37:59.178][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 20:37:59.179][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 20:37:59.181][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 20:37:59.182][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 20:37:59.183][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 20:37:59.184][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 20:37:59.186][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 20:37:59.187][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:59.188][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:59.189][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 20:37:59.191][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 20:37:59.192][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 20:37:59.193][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 20:37:59.195][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 20:37:59.196][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 20:37:59.197][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 20:37:59.199][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 20:37:59.200][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 20:37:59.201][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 20:37:59.203][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 20:37:59.204][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 20:37:59.205][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 20:37:59.207][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 20:37:59.208][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 20:37:59.209][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 20:37:59.211][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 20:37:59.212][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 20:37:59.212][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.214][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.221][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.DEBUG[2024-05-17 20:37:59.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.238][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[2024-05-17 20:37:59.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.250][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[2024-05-17 20:37:59.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.261][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[2024-05-17 20:37:59.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.295][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[2024-05-17 20:37:59.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 20:37:59.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 20:37:59.319][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-17 20:37:59.320][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-17 20:37:59.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:59.323][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.325][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 20:37:59.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.328][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.328][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-17 20:37:59.329][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-17 20:37:59.330][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 20:37:59.331][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.332][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-17 20:37:59.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-17 20:37:59.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-17 20:37:59.335][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 20:37:59.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 20:37:59.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 20:37:59.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 20:37:59.337][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-17 20:37:59.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:59.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:59.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 20:37:59.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 20:37:59.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 20:37:59.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 20:37:59.343][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-17 20:37:59.343][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-17 20:37:59.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 20:37:59.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 20:37:59.345][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 20:37:59.346][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-17 20:37:59.346][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-17 20:37:59.347][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 20:37:59.349][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 20:37:59.350][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-17 20:37:59.352][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 20:37:59.353][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 20:37:59.355][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 20:37:59.357][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-17 20:37:59.358][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-17 20:37:59.359][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-17 20:37:59.361][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-17 20:37:59.362][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:59.363][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-17 20:37:59.364][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-17 20:37:59.365][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-17 20:37:59.366][biodb::testThat]
biodb.INFO [2024-05-17 20:37:59.367][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-17 20:37:59.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 20:37:59.369][biodb::testThat]
biodb.DEBUG[2024-05-17 20:37:59.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-17 20:37:59.375][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:59.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-17 20:37:59.377][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:59.378][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-17 20:37:59.382][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[2024-05-17 20:37:59.384][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 20:37:59.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-17 20:37:59.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:59.388][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-17 20:37:59.392][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-17 20:37:59.393][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 20:37:59.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-17 20:37:59.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 20:37:59.397][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-05-17 20:37:59.398][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 20:37:59.400][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-17 20:37:59.401][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-17 20:37:59.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 20:37:59.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 20:37:59.415][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.416][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.417][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.423][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:59.424][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:59.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.425][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.427][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-17 20:37:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-17 20:37:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.431][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:59.432][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:59.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 20:37:59.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 20:37:59.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.439][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-17 20:37:59.440][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-17 20:37:59.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.442][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.444][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-17 20:37:59.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-17 20:37:59.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.447][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:59.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:59.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.451][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.452][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:59.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 20:37:59.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.456][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:59.457][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:59.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-17 20:37:59.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 20:37:59.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.464][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:59.465][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:59.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.467][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:59.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 20:37:59.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.472][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:59.473][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:59.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.475][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 20:37:59.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 20:37:59.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.481][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:59.482][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:59.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.483][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.485][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-17 20:37:59.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-17 20:37:59.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.489][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:59.490][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:59.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.491][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.493][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-17 20:37:59.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-17 20:37:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 20:37:59.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 20:37:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 20:37:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 20:37:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 20:37:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 20:37:59.535][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-17 20:37:59.538][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 20:37:59.539][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-17 20:37:59.540][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-17 20:37:59.541][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 20:37:59.542][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 20:37:59.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 20:37:59.544][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 20:37:59.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 20:37:59.545][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 20:37:59.546][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 369 ]
> 
> proc.time()
   user  system elapsed 
 17.616   1.040  30.565

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.9490.0932.126
ChebiEntry0.1340.0000.135