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This page was generated on 2023-05-10 10:04:27 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for biodbChebi on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 191/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.7.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 8404aa9
git_last_commit_date: 2023-04-25 15:32:59 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: biodbChebi
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.7.0.tar.gz
StartedAt: 2023-05-09 09:57:36 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 10:03:38 -0000 (Tue, 09 May 2023)
EllapsedTime: 362.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbChebi_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 2.784  0.288   7.675
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘biodbChebi.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-05-09 09:58:31.305][biodb::testContext]
biodb.INFO [2023-05-09 09:58:31.308][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 09:58:31.309][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-09 09:58:31.310][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 09:58:31.312][biodb::testContext]
biodb.INFO [2023-05-09 09:58:31.333][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 09:58:31.336][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 09:58:31.346][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:58:31.347][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 09:58:31.349][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.354][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 09:58:31.381][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.386][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 09:58:31.387][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.392][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 09:58:31.394][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 09:58:31.395][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 09:58:31.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.399][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.DEBUG[2023-05-09 09:58:31.400][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 09:58:31.401][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 09:58:31.403][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.408][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 09:58:31.409][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 09:58:31.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.414][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 09:58:31.415][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 09:58:31.417][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 09:58:31.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.422][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 09:58:31.423][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.427][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.DEBUG[2023-05-09 09:58:31.428][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 09:58:31.429][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 09:58:31.431][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 09:58:31.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.436][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 09:58:31.437][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 09:58:31.438][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 09:58:31.440][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 09:58:31.441][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 09:58:31.442][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 09:58:31.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.446][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[2023-05-09 09:58:31.448][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 09:58:31.449][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 09:58:31.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.454][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 09:58:31.455][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 09:58:31.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.459][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[2023-05-09 09:58:31.460][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 09:58:31.462][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 09:58:31.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.467][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 09:58:31.468][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 09:58:31.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.472][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[2023-05-09 09:58:31.473][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 09:58:31.475][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 09:58:31.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.479][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 09:58:31.481][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 09:58:31.486][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 09:58:31.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.489][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[2023-05-09 09:58:31.491][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 09:58:31.492][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 09:58:31.494][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 09:58:31.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.502][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 09:58:31.551][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.586][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-09 09:58:31.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:58:31.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.592][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.593][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.594][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.595][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 09:58:31.597][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:58:31.598][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.599][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 09:58:31.601][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:58:31.602][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.603][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.604][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:58:31.604][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:58:31.604][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 09:58:31.604][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 09:58:31.604][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 09:58:31.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:58:31.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.609][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:58:31.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.614][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:58:31.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:58:31.618][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.619][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.621][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 09:58:31.623][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.624][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 09:58:31.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:58:31.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.630][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.631][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.632][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.633][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 09:58:31.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:58:31.636][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.637][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 09:58:31.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:58:31.640][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.641][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.642][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:58:31.642][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:58:31.642][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 09:58:31.642][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 09:58:31.642][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 09:58:31.643][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:58:31.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:58:31.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.652][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.653][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:58:31.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:58:31.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.656][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.658][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 09:58:31.660][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.661][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-09 09:58:31.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:58:31.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.668][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.670][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 09:58:31.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:58:31.673][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.674][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 09:58:31.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:58:31.676][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.677][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.679][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.680][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:58:31.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:58:31.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.687][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.688][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:58:31.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:58:31.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.693][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.694][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 09:58:31.696][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.698][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 09:58:31.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:58:31.702][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.707][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 09:58:31.708][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:58:31.709][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.710][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 09:58:31.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:58:31.713][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.715][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:31.716][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.718][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:58:31.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:58:31.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:31.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:31.725][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:58:31.727][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:58:31.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:58:31.731][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:31.732][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:58:31.737][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:58:31.738][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.751][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.DEBUG[2023-05-09 09:58:31.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.819][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[2023-05-09 09:58:31.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:31.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:31.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:31.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:31.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:31.836][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.DEBUG[2023-05-09 09:58:31.837][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 09:58:31.843][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 09:58:31.845][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 09:58:31.847][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 09:58:31.849][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 09:58:31.850][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 09:58:31.852][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 09:58:31.854][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 09:58:31.856][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 09:58:31.857][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 09:58:31.859][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 09:58:31.861][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 09:58:31.863][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 09:58:31.864][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 09:58:31.866][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 09:58:31.868][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 09:58:31.870][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 09:58:31.872][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 09:58:31.873][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 09:58:31.875][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 09:58:31.877][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 09:58:31.879][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 09:58:31.881][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 09:58:31.883][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 09:58:31.884][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 09:58:31.886][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 09:58:31.888][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 09:58:31.889][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 09:58:31.899][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 09:58:31.901][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 09:58:31.903][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 09:58:31.905][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 09:58:31.907][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 09:58:31.909][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 09:58:31.911][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 09:58:31.912][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 09:58:31.914][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 09:58:31.916][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 09:58:31.918][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 09:58:31.920][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 09:58:31.922][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 09:58:31.924][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 09:58:31.925][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 09:58:31.927][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 09:58:31.929][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 09:58:31.931][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 09:58:31.933][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 09:58:31.935][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 09:58:31.937][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 09:58:31.938][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 09:58:31.940][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 09:58:31.942][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 09:58:31.944][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 09:58:31.946][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 09:58:31.947][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 09:58:31.949][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 09:58:31.951][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 09:58:31.953][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 09:58:31.955][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 09:58:31.957][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 09:58:31.959][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 09:58:31.961][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 09:58:31.962][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 09:58:31.964][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 09:58:31.966][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 09:58:31.968][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 09:58:31.970][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 09:58:31.972][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 09:58:31.974][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 09:58:31.975][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 09:58:31.977][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 09:58:31.979][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 09:58:31.981][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 09:58:31.983][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 09:58:31.984][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 09:58:31.986][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 09:58:31.988][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 09:58:31.990][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 09:58:31.991][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 09:58:31.993][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 09:58:31.995][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 09:58:31.997][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 09:58:31.999][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 09:58:32.007][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 09:58:32.009][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 09:58:32.013][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:58:32.014][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.016][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.088][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.DEBUG[2023-05-09 09:58:32.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.112][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[2023-05-09 09:58:32.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.128][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.DEBUG[2023-05-09 09:58:32.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:58:32.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:32.164][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-09 09:58:32.177][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-09 09:58:32.180][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:32.181][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 09:58:32.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:32.184][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:58:32.185][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:32.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:58:32.188][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:32.189][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-09 09:58:32.190][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-09 09:58:32.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:58:32.193][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:32.194][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-09 09:58:32.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-09 09:58:32.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-09 09:58:32.198][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 09:58:32.199][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:58:32.199][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:58:32.199][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 09:58:32.200][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-09 09:58:32.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:32.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:32.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:58:32.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:58:32.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:58:32.207][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:58:32.209][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:58:32.209][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-09 09:58:32.210][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:58:32.211][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:58:32.212][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 09:58:32.214][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-09 09:58:32.214][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-09 09:58:32.230][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 09:58:32.233][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 09:58:32.235][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-09 09:58:32.237][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 09:58:32.239][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 09:58:32.241][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 09:58:32.274][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-09 09:58:32.275][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-09 09:58:32.281][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-09 09:58:32.287][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-09 09:58:32.292][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 09:58:32.294][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 09:58:32.296][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-09 09:58:32.298][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-09 09:58:32.320][biodb::testThat]
biodb.INFO [2023-05-09 09:58:32.322][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-05-09 09:58:32.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:32.324][biodb::testThat]
biodb.TRACE[2023-05-09 09:58:32.330][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-05-09 09:58:32.337][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:32.342][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:32.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:32.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:32.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:32.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:32.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:32.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:32.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:32.390][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.393][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.394][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.422][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:32.424][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:32.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.427][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.463][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:32.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:32.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.473][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:32.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:32.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.477][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:32.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:32.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:32.490][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:32.491][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.493][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:32.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:32.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.504][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.505][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.508][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:32.521][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:32.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.524][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.525][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:32.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:32.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.535][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:32.536][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.539][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:32.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.551][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:32.552][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:32.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.555][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:32.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:32.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.567][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:32.568][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:32.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.571][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:32.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:32.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.582][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:32.584][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:32.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.586][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.588][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.612][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:32.614][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:32.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.617][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:32.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:32.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:32.736][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-05-09 09:58:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:32.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:32.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:32.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:32.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:32.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:32.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:32.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:32.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:32.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:32.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:32.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.984][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.989][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:32.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:32.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:32.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:32.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.024][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.025][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.057][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.061][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.093][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.097][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.128][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.130][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.132][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.166][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.167][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.168][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.184][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.190][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.196][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.201][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.202][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.204][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.244][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.245][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.260][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.266][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.272][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.277][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.281][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.282][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.297][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.302][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.308][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.314][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.315][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.316][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.317][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.345][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.354][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.355][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.385][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.387][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.388][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.389][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.423][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.426][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.443][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.447][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.454][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.456][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.458][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.466][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.467][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.470][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.477][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.479][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.482][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.489][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.491][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.493][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.505][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.512][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.514][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.516][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.525][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.528][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.543][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.545][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.546][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.547][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.555][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.559][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.567][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.569][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.571][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:58:33.581][biodb::testThat]
biodb.INFO [2023-05-09 09:58:33.582][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-09 09:58:33.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:33.585][biodb::testThat]
biodb.DEBUG[2023-05-09 09:58:33.604][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-05-09 09:58:33.614][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:33.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-05-09 09:58:33.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:33.624][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-05-09 09:58:33.626][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:33.690][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:33.692][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:33.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:33.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:33.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:33.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:33.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:33.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:33.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:33.712][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.713][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.716][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.749][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.750][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.753][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.755][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:33.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.763][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.767][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:33.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:33.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.778][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.782][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:33.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.793][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.794][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.797][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:33.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.807][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.809][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.811][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.823][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:33.824][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.827][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.829][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:33.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:33.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.850][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.853][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:33.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.865][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.866][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.867][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.869][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:33.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:33.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.880][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:33.882][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.884][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:33.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:33.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.896][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.897][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.900][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:33.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:33.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:33.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:33.967][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-05-09 09:58:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-09 09:58:33.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-09 09:58:33.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-09 09:58:33.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-09 09:58:33.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:33.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-09 09:58:33.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-09 09:58:33.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:33.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 09:58:33.992][biodb::testThat]
biodb.INFO [2023-05-09 09:58:33.993][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-09 09:58:33.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:33.995][biodb::testThat]
biodb.TRACE[2023-05-09 09:58:33.999][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.000][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.003][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:34.005][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-05-09 09:58:34.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:34.060][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-05-09 09:58:34.076][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-09 09:58:34.104][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:34.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-09 09:58:34.136][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:34.138][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-09 09:58:34.171][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:34.175][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:34.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:58:34.178][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:34.181][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-09 09:58:34.183][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-05-09 09:58:34.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:34.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:34.204][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.205][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.206][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.208][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.210][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:58:34.213][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.214][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-05-09 09:58:34.215][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:34.216][biodb::testThat]
biodb.TRACE[2023-05-09 09:58:34.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:34.357][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:34.361][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:34.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:58:34.365][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:34.367][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-05-09 09:58:34.399][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.400][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-05-09 09:58:34.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:34.403][biodb::testThat]
biodb.TRACE[2023-05-09 09:58:34.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:34.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:34.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:34.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:34.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:34.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.492][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:34.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:34.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:34.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:34.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:34.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:34.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:34.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:34.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.568][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:58:34.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:34.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:58:34.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:34.580][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:34.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:58:34.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:34.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 09:58:34.590][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.591][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-09 09:58:34.593][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:34.594][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.601][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.603][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-09 09:58:34.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:34.606][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.613][biodb::testThat]
biodb.INFO [2023-05-09 09:58:34.615][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-09 09:58:34.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:34.617][biodb::testThat]
biodb.DEBUG[2023-05-09 09:58:34.622][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-05-09 09:58:37.374][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-05-09 09:58:40.804][biodb::testThat]
biodb.INFO [2023-05-09 09:58:40.807][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-09 09:58:40.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:40.811][biodb::testThat]
biodb.DEBUG[2023-05-09 09:58:42.816][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2023-05-09 09:58:45.120][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:45.123][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:45.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.127][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.129][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:45.131][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:45.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.134][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:58:45.138][biodb::testThat]
biodb.INFO [2023-05-09 09:58:45.139][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-05-09 09:58:45.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:58:45.143][biodb::testThat]
biodb.TRACE[2023-05-09 09:58:45.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:45.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:45.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:45.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:45.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:45.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:45.376][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:45.382][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:45.384][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:58:45.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:45.389][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-09 09:58:45.494][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:45.498][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:45.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:58:45.501][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:45.503][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-05-09 09:58:45.526][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 09:58:45.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 09:58:45.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:45.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:45.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:45.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:45.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:45.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:45.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-09 09:58:45.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:45.664][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-09 09:58:45.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:45.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:45.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:45.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:45.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:45.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:45.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:45.684][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-05-09 09:58:45.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:45.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-05-09 09:58:45.758][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:58:45.760][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:58:45.761][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:45.763][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:58:45.764][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:58:45.766][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:58:45.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:45.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:45.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:45.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:45.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:45.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:45.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:45.786][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-05-09 09:58:45.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:58:45.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:58:45.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-05-09 09:58:49.818][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-05-09 09:58:52.518][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:58:52.527][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-05-09 09:58:52.557][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-05-09 09:58:52.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-05-09 09:58:52.576][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:58:52.602][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:52.604][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:52.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:52.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:52.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:52.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:52.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:52.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:52.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:52.623][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.627][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.638][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:52.639][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:52.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.642][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.644][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:52.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.653][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:52.654][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:52.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.657][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.659][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.668][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:52.670][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:52.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.672][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:52.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.683][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:52.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:52.686][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.687][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:52.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.698][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:52.699][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:52.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.702][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.704][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:52.713][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.719][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:52.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.730][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:52.732][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:52.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.735][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.745][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:52.747][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:52.748][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.750][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:52.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:52.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.761][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:52.762][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:52.763][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.765][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.767][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:52.777][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:52.778][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.780][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:52.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:52.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:52.849][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-05-09 09:58:52.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:52.890][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:52.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:52.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-09 09:58:52.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:52.903][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-09 09:58:52.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:52.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:52.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:52.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:52.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:52.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:52.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:52.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:52.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:52.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:52.985][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:52.987][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-09 09:58:52.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:52.991][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-09 09:58:53.051][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:58:53.055][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:58:53.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:58:53.059][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:53.061][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-09 09:58:53.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:53.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:53.134][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-05-09 09:58:53.136][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:53.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-05-09 09:58:53.140][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:53.143][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml".
biodb.DEBUG[2023-05-09 09:58:53.144][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:53.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:53.172][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:53.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:53.192][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.196][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.207][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:53.209][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:53.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.211][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.213][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:53.214][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:53.216][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.217][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:53.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:53.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.223][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.225][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.234][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.237][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.239][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.240][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.243][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.244][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:53.246][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.248][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.250][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.254][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.256][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.257][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.260][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.271][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.272][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.275][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.277][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:53.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:53.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.290][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.350][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-05-09 09:58:53.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:53.395][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-05-09 09:58:53.396][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:53.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-05-09 09:58:53.400][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:53.403][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml".
biodb.DEBUG[2023-05-09 09:58:53.404][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:53.430][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:53.432][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:53.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:53.451][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.452][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.454][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.455][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.465][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:53.475][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:53.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.478][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.479][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:53.481][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:53.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.483][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.485][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:53.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:53.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.489][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.491][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.492][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.495][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.496][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.500][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.502][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:53.504][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.506][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.509][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.512][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.513][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.515][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.516][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.517][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.528][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.530][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.533][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.543][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:53.545][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:53.546][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.547][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.606][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-05-09 09:58:53.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:53.650][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-05-09 09:58:53.652][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:53.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-05-09 09:58:53.656][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:53.658][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml".
biodb.DEBUG[2023-05-09 09:58:53.660][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:53.686][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:53.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:53.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:53.714][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.717][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.718][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.729][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:53.731][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:53.732][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.733][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.735][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:53.736][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:53.738][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.739][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.741][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:53.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:53.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.745][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.748][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:53.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.751][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.752][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:53.755][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.756][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.758][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:53.760][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.761][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.762][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:53.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.768][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.769][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.771][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.772][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.773][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.785][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.786][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.789][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.791][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:53.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:53.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.800][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:53.801][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:53.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.804][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.864][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-05-09 09:58:53.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:53.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:53.908][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-05-09 09:58:53.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:53.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-05-09 09:58:53.913][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:53.916][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml".
biodb.DEBUG[2023-05-09 09:58:53.917][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:53.943][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:53.953][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:53.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:53.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:53.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:53.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:53.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:53.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:53.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:53.973][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.974][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.977][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.988][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:53.989][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:53.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.992][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:53.993][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:53.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:53.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:53.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.003][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.004][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.007][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.018][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.022][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.033][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.035][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.037][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.048][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.052][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.054][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.063][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.065][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.066][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.067][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.069][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.078][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.080][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.082][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.093][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.097][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.109][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.110][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.113][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.123][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.128][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.220][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-05-09 09:58:54.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:54.254][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-05-09 09:58:54.256][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:54.258][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-05-09 09:58:54.260][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:54.263][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml".
biodb.DEBUG[2023-05-09 09:58:54.264][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:54.292][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:54.294][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:54.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:54.315][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.316][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.319][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.330][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.332][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.334][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.336][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.346][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.347][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.349][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.350][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.362][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.363][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.366][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.377][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.379][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.380][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.381][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.393][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.394][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.397][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.399][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.408][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.410][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.413][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.424][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.428][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.439][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.442][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.444][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.457][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.467][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.479][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.483][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.552][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-05-09 09:58:54.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:54.585][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-05-09 09:58:54.586][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:54.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-05-09 09:58:54.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:54.593][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml".
biodb.DEBUG[2023-05-09 09:58:54.594][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:54.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:54.622][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:54.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:54.641][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.643][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.644][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.645][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.656][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.657][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.660][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.662][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.671][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.673][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.675][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:54.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.688][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.689][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.690][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:54.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:54.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.709][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.713][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.714][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:54.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.725][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.727][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:54.728][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.730][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.731][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.733][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.736][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.747][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.751][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:54.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.762][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.767][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.778][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.782][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:54.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:54.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.793][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.798][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:54.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.869][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-05-09 09:58:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:54.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:54.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:54.904][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-05-09 09:58:54.906][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:54.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-05-09 09:58:54.910][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:54.912][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2023-05-09 09:58:54.914][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:54.941][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:54.943][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:54.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:54.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:54.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:54.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:54.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:54.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:54.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:54.972][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.974][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.976][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:54.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.988][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.989][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.992][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:54.994][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:54.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:54.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.003][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.005][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.007][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.022][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.023][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.034][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.036][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.038][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.049][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.051][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.054][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.056][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.059][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.060][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.062][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.071][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.073][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.074][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.076][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.087][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.091][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.104][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.107][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.109][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.118][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.122][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.124][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.193][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-05-09 09:58:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:55.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:55.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:55.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:55.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:55.237][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-05-09 09:58:55.238][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:55.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-05-09 09:58:55.243][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:55.245][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2023-05-09 09:58:55.247][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:55.274][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:55.276][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:55.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:55.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:55.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:55.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:55.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:55.296][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.297][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.300][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.311][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:55.313][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:55.314][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.315][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:55.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:55.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.327][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.328][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.331][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.342][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.344][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.345][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.347][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.360][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.362][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.374][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.375][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.377][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.378][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.380][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.381][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.384][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.386][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.395][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.397][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.398][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.399][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.411][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.415][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.426][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.428][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.429][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.430][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.432][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.442][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.443][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.446][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.448][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.526][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-05-09 09:58:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:55.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:55.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:55.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:55.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:55.560][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-05-09 09:58:55.561][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:55.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-05-09 09:58:55.565][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:55.568][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2023-05-09 09:58:55.570][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:55.596][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:55.598][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:55.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:55.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:55.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:55.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:55.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:55.618][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.622][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.633][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:55.635][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:55.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.638][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.640][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:55.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.650][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.651][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.654][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:55.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.666][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.667][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.670][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:55.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:55.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.681][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.684][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.686][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:55.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.698][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.699][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:55.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.702][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.704][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.707][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.752][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.765][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.768][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.770][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.781][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.786][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:55.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.798][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.803][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:55.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.815][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.816][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.818][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.819][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:55.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:55.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:55.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.902][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-05-09 09:58:55.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:55.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:55.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:55.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:55.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:55.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:55.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:55.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:55.944][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-05-09 09:58:55.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:55.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-05-09 09:58:55.951][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:58:55.954][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2023-05-09 09:58:55.956][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:55.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:58:55.990][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:58:55.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:55.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:55.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:56.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:56.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:56.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:56.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:58:56.013][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.017][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.029][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:56.031][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:56.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.050][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.052][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:58:56.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:58:56.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.063][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:56.065][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:56.066][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.068][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:58:56.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:58:56.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:56.082][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:56.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.085][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:58:56.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:58:56.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:56.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:56.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.103][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:58:56.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:58:56.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.115][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:56.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:58:56.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.120][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.122][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:56.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.125][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.127][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.129][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:58:56.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:56.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:56.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.144][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:58:56.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.156][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:56.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:56.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.161][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:58:56.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:58:56.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.174][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:56.176][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:56.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.179][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.181][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:58:56.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:58:56.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.192][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:56.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:56.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.197][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:58:56.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:58:56.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:58:56.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:58:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:58:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:56.277][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-05-09 09:58:56.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:58:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:58:56.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:58:56.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:58:56.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:56.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:56.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:56.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:56.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:56.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:56.314][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[2023-05-09 09:58:56.316][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-05-09 09:58:56.318][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:58:56.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.INFO [2023-05-09 09:58:56.322][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-05-09 09:58:56.333][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:58:56.335][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:58:56.337][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:58:56.339][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:58:56.341][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:58:56.342][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:58:56.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:58:56.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:58:56.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:58:56.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:58:56.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:58:56.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:58:56.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:58:56.382][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-05-09 09:58:56.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:58:56.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:58:56.428][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-05-09 09:58:58.989][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-05-09 09:59:01.414][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:01.423][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-05-09 09:59:01.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-05-09 09:59:01.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-05-09 09:59:01.457][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:01.484][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:01.485][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:01.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:01.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:01.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:01.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:01.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:01.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:01.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:01.517][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.520][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.521][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.532][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:01.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:01.535][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.536][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.538][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:01.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:01.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.547][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:01.549][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:01.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.552][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.553][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:01.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.563][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:01.564][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:01.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.567][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:01.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:01.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.573][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:01.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:01.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.579][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.580][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:01.582][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.583][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.585][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.586][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:01.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:01.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:01.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.600][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:01.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:01.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.610][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:01.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:01.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.615][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:01.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:01.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.626][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:01.627][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:01.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.630][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.632][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:01.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:01.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:01.642][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:01.644][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.645][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:01.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:01.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:01.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:01.707][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-05-09 09:59:01.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:01.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:01.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:01.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:01.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:01.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:01.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:01.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:01.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:01.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:01.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:01.741][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-05-09 09:59:01.750][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:01.753][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-05-09 09:59:01.755][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:01.756][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:01.758][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:01.759][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:01.761][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:01.762][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:01.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:01.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:01.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:01.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:01.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:01.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:01.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:01.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-05-09 09:59:01.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:01.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:01.789][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-05-09 09:59:03.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-05-09 09:59:05.233][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-05-09 09:59:05.239][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-05-09 09:59:05.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-05-09 09:59:05.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-05-09 09:59:05.271][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-05-09 09:59:05.276][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:05.302][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:05.304][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:05.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:05.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:05.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:05.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:05.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:05.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:05.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:05.323][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.327][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.338][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:05.339][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:05.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.342][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.344][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:05.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.353][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:05.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:05.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.357][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:05.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:05.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.368][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:05.369][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:05.371][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.372][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.385][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:05.387][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:05.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.390][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.392][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:05.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:05.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.396][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.397][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:05.399][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.400][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.402][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.412][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:05.414][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:05.415][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.416][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:05.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.427][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:05.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:05.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.431][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:05.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.443][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:05.444][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:05.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.447][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.448][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:05.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:05.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.458][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:05.459][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:05.460][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.462][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:05.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:05.522][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-05-09 09:59:05.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:05.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:05.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:05.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:05.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:05.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:05.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:05.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:05.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:05.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:05.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:05.555][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-05-09 09:59:05.557][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:05.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-05-09 09:59:05.561][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:05.562][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:05.564][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:05.565][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:05.566][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:05.568][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:05.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:05.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:05.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:05.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:05.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:05.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:05.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:05.587][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-05-09 09:59:05.591][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:05.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:05.594][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-05-09 09:59:06.869][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-05-09 09:59:08.318][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:08.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-05-09 09:59:08.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-05-09 09:59:08.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-05-09 09:59:08.363][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:08.391][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:08.393][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:08.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:08.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:08.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:08.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:08.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:08.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:08.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:08.414][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.417][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.418][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.429][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:08.431][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.434][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.436][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:08.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:08.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.445][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:08.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:08.448][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.449][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:08.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:08.462][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:08.464][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.465][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:08.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:08.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.476][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:08.478][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:08.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.481][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:08.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:08.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.492][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:08.494][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:08.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.496][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.498][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:08.500][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.503][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.504][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.514][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:08.516][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:08.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.518][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.530][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:08.531][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:08.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.534][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.555][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:08.557][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:08.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.560][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:08.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:08.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.571][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:08.572][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:08.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.575][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.577][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:08.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:08.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:08.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:08.646][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-05-09 09:59:08.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:08.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:08.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:08.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:08.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:08.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:08.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:08.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:08.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:08.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:08.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:08.680][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-05-09 09:59:08.681][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:08.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-05-09 09:59:08.685][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:08.687][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:08.688][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:08.690][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:08.691][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:08.693][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:08.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:08.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:08.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:08.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:08.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:08.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:08.711][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[2023-05-09 09:59:08.712][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-05-09 09:59:08.716][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:08.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:08.719][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-05-09 09:59:11.890][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-05-09 09:59:14.314][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:14.335][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-05-09 09:59:14.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-05-09 09:59:14.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-05-09 09:59:14.369][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:14.396][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:14.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:14.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:14.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:14.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:14.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:14.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:14.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:14.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:14.417][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.418][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.421][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.432][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:14.433][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:14.435][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.436][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:14.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:14.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.447][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:14.448][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:14.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.451][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.462][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:14.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:14.464][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.466][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:14.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:14.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.476][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:14.478][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:14.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.480][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:14.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:14.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:14.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:14.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.495][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.497][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:14.499][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.501][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.503][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:14.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:14.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.516][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:14.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:14.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.527][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:14.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:14.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.531][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:14.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:14.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.542][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:14.544][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:14.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.546][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.548][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:14.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.557][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:14.559][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:14.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.561][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:14.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:14.640][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-05-09 09:59:14.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:14.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:14.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:14.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:14.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:14.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:14.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:14.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:14.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:14.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:14.674][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-05-09 09:59:14.675][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:14.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-05-09 09:59:14.679][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:14.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:14.682][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:14.684][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:14.685][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:14.687][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:14.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:14.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:14.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:14.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:14.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:14.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:14.705][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[2023-05-09 09:59:14.706][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-05-09 09:59:14.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:14.711][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:14.713][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-05-09 09:59:16.323][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-05-09 09:59:17.852][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:17.861][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-05-09 09:59:17.875][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-05-09 09:59:17.888][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-05-09 09:59:17.901][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:17.932][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:17.933][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:17.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:17.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:17.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:17.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:17.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:17.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:17.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:17.953][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:17.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:17.955][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.957][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:17.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.968][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:17.969][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:17.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.972][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:17.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.983][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:17.984][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:17.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.987][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:17.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:17.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:17.998][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:17.999][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:18.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.002][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:18.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:18.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.013][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:18.014][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:18.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.017][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:18.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.028][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:18.029][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:18.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.032][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.034][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:18.035][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.038][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.039][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:18.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.049][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:18.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:18.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.053][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.064][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:18.065][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:18.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.068][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.079][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:18.081][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:18.082][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.083][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.085][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:18.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:18.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.094][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:18.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:18.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.098][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:18.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:18.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:18.178][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-05-09 09:59:18.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:18.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:18.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:18.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:18.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:18.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:18.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:18.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:18.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:18.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:18.212][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-05-09 09:59:18.214][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:18.216][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-05-09 09:59:18.218][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:18.219][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:18.221][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:18.222][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:18.224][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:18.225][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:18.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:18.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:18.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:18.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:18.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:18.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:18.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:18.245][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-05-09 09:59:18.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:18.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:18.252][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-05-09 09:59:20.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-05-09 09:59:24.268][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:24.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-05-09 09:59:24.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-05-09 09:59:24.305][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-05-09 09:59:24.310][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:24.335][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:24.337][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:24.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:24.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:24.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:24.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:24.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:24.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:24.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:24.370][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.372][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.373][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.375][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.386][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:24.388][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:24.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.390][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.392][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:24.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.401][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:24.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:24.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.406][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:24.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:24.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.417][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:24.419][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:24.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.421][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:24.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:24.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.433][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:24.434][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:24.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.437][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:24.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:24.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:24.450][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:24.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.452][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.454][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:24.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.459][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.460][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:24.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.470][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:24.471][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:24.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.474][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:24.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.485][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:24.487][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:24.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.489][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:24.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.501][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:24.502][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:24.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.505][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.507][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:24.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:24.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.516][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:24.517][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:24.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.520][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.522][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:24.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:24.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:24.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:24.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:24.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:24.603][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-05-09 09:59:24.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:24.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:24.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:24.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:24.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:24.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:24.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:24.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:24.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:24.657][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[2023-05-09 09:59:24.658][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-05-09 09:59:24.660][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:24.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-05-09 09:59:24.664][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:24.666][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:24.667][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:24.669][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:24.671][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:24.672][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:24.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:24.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:24.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:24.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:24.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:24.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:24.691][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[2023-05-09 09:59:24.693][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-05-09 09:59:24.697][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:24.698][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:24.700][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-05-09 09:59:26.958][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-05-09 09:59:28.957][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:28.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-05-09 09:59:28.981][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-05-09 09:59:28.995][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-05-09 09:59:29.000][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:29.026][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:29.028][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:29.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:29.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:29.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:29.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:29.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:29.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:29.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:29.047][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.050][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.051][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.062][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:29.063][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:29.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.066][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:29.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.088][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:29.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:29.091][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.093][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:29.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:29.105][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:29.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.107][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:29.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:29.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.118][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:29.119][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:29.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.122][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:29.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:29.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.133][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:29.134][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:29.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.137][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.138][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:29.140][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.141][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.143][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.144][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:29.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.153][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:29.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:29.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.157][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:29.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.168][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:29.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:29.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.172][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.183][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:29.184][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:29.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.187][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.189][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:29.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.198][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:29.199][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:29.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.202][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:29.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:29.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:29.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:29.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:29.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:29.270][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-05-09 09:59:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:29.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:59:29.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:29.349][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:29.352][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 09:59:32.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 09:59:37.061][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:37.071][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-05-09 09:59:37.087][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-05-09 09:59:37.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:37.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:37.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:37.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:37.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:37.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:37.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:37.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:37.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:37.968][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:59:37.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:37.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:37.979][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 09:59:41.730][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 09:59:44.504][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:44.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-05-09 09:59:44.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-05-09 09:59:44.537][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:59:44.541][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:44.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:44.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 09:59:46.269][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 09:59:48.071][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:48.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-05-09 09:59:48.099][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-05-09 09:59:48.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:48.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:48.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:48.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:48.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:48.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:48.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:48.126][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-05-09 09:59:48.127][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:48.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-05-09 09:59:48.132][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:48.133][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:48.135][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:48.137][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:48.138][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:48.140][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:48.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:48.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:48.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:48.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:48.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:48.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:48.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:48.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-05-09 09:59:48.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:48.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:48.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-05-09 09:59:50.812][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-05-09 09:59:53.365][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:53.376][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-05-09 09:59:53.392][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-05-09 09:59:53.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-05-09 09:59:53.413][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:53.442][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:53.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:53.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:53.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:53.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:53.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:53.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:53.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:53.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:53.464][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.467][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.469][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.480][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:53.481][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:53.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.484][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:53.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.495][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:53.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:53.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.499][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:53.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.510][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:53.512][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:53.513][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.515][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:53.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:53.527][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:53.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.530][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.540][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:53.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:53.543][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.545][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.546][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:53.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.556][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:53.569][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:53.575][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.577][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:53.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:53.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.589][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.594][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.606][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:53.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:53.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.610][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:53.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.622][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:53.624][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:53.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.627][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.638][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:53.640][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:53.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.642][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:53.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:53.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:53.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:53.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:53.713][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-05-09 09:59:53.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:53.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:53.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:53.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:53.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:53.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:53.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:53.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:53.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:53.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:53.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:53.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:53.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:53.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:53.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:53.805][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-05-09 09:59:53.807][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:53.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-05-09 09:59:53.813][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 09:59:53.815][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 09:59:53.817][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:53.818][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 09:59:53.820][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 09:59:53.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 09:59:53.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:53.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:53.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:53.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:53.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:53.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:53.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:53.848][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-05-09 09:59:53.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:53.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:53.912][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-05-09 09:59:55.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-05-09 09:59:58.208][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:58.218][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-05-09 09:59:58.234][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-05-09 09:59:58.249][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-05-09 09:59:58.255][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 09:59:58.285][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:58.287][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 09:59:58.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.309][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.311][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.312][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.314][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.326][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:58.327][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:58.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.330][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 09:59:58.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 09:59:58.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.342][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:58.344][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:58.345][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.346][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:58.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:58.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.357][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:58.358][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:58.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.361][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 09:59:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 09:59:58.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.372][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:58.373][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:58.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.376][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 09:59:58.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 09:59:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.387][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:58.388][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:58.390][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.391][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.393][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:58.394][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:58.395][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.397][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 09:59:58.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:58.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.421][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.422][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.425][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.436][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:58.438][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:58.439][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.440][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:58.453][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:58.454][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.455][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 09:59:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 09:59:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:58.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:58.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.470][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 09:59:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 09:59:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.540][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-05-09 09:59:58.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:59:58.615][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:59:58.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:59:58.618][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:58.620][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-09 09:59:58.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:58.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:58.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:58.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:58.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:58.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:58.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:58.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:58.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:58.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:58.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:58.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.379][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 09:59:59.384][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:59:59.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-09 09:59:59.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:59.389][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-09 09:59:59.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:59.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:59.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:59.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:59.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:59.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:59.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:59.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:59.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:59.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:59.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:59.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:00.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:00.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:00.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:00.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:00.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:00.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:00.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:00.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:00.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:00.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:00.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:00.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:00.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:00.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:00.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:00.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:00.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:00.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:00.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:00.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:00.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.125][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:00:00.147][biodb::testThat]
biodb.INFO [2023-05-09 10:00:00.148][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-05-09 10:00:00.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:00.151][biodb::testThat]
biodb.TRACE[2023-05-09 10:00:00.155][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:00:00.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:00:00.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:00.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:00.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:00.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:00.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:00.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:00.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:00.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:00.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:00.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:00.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:00.280][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:00.283][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:00:03.499][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:00:05.765][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:05.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-05-09 10:00:05.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-05-09 10:00:05.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:05.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:05.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:05.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:05.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:05.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:05.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:05.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:05.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:05.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:05.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:05.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:05.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:05.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:05.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:05.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:00:08.269][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:00:10.591][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:10.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-05-09 10:00:10.626][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-05-09 10:00:10.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:10.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:10.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:10.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:10.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:10.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:10.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:10.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:10.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:10.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:10.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:10.683][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:10.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:10.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:10.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:00:14.176][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:00:18.116][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:18.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-05-09 10:00:18.149][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-05-09 10:00:18.157][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:18.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:18.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:18.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:18.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:18.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:18.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:18.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:18.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.220][private$selectFields]
biodb.TRACE[2023-05-09 10:00:18.221][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:18.223][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:18.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.229][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.233][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.235][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.243][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.244][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.274][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-09 10:00:18.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:18.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:18.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:18.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:18.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:18.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:18.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:18.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.301][private$selectFields]
biodb.TRACE[2023-05-09 10:00:18.303][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:18.304][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:18.305][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.308][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.310][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.311][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.319][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.327][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.329][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.331][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:18.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.338][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.339][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:18.362][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:18.363][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:18.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:18.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:18.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:18.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:18.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:18.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:18.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:18.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:18.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:18.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:18.584][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:18.589][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:18.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:18.593][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:00:22.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:00:31.957][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:31.968][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-05-09 10:00:31.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-05-09 10:00:31.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:31.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:31.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:32.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:00:34.256][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:00:37.514][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:37.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-05-09 10:00:37.540][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-05-09 10:00:37.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:37.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:37.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:37.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:37.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:37.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:37.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:37.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:37.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:37.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:37.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:37.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:37.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:37.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:37.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:37.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:37.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:37.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:37.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:37.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:37.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:37.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:37.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:37.681][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:37.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:37.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:37.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:37.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:37.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:37.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:37.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:37.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.787][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.789][private$selectFields]
biodb.TRACE[2023-05-09 10:00:37.791][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:37.793][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:37.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.799][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.803][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.807][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.811][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.813][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.815][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.816][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.818][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.823][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.825][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.851][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-09 10:00:37.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:37.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:37.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:37.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:37.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:37.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:37.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:37.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.951][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.953][private$selectFields]
biodb.TRACE[2023-05-09 10:00:37.954][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:37.956][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:37.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:37.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.962][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.964][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.965][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:37.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:37.972][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:37.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.017][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.020][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.023][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.024][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.043][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:38.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.072][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.073][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.074][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.076][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.077][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.083][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.086][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.088][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.091][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.092][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.096][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.116][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-09 10:00:38.117][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:38.118][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:38.130][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:38.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:38.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:00:38.138][biodb::testThat]
biodb.INFO [2023-05-09 10:00:38.139][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-05-09 10:00:38.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:38.142][biodb::testThat]
biodb.TRACE[2023-05-09 10:00:38.147][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:00:38.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:00:38.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:38.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:38.279][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:38.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-09 10:00:38.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:38.285][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-09 10:00:38.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:38.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:38.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-09 10:00:38.334][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:38.336][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-09 10:00:38.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:38.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.376][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:38.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:38.382][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-09 10:00:38.384][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:38.386][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-09 10:00:38.390][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:38.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.421][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.422][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.424][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.425][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.427][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.428][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.432][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.438][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.441][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.443][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.447][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.449][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.470][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-09 10:00:38.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.506][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.507][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.509][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.516][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.517][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.534][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.536][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.538][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.542][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.543][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.545][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.547][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.567][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:38.568][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:38.569][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:38.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:38.682][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:38.687][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:38.688][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-05-09 10:00:38.690][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:38.692][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-05-09 10:00:38.696][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:38.700][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:38.702][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-05-09 10:00:38.704][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:38.706][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-05-09 10:00:38.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:38.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:38.818][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:38.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.849][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.850][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.852][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.853][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.858][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.860][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.864][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.868][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.872][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.873][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.891][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-09 10:00:38.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.922][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.923][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.924][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.925][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.927][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.928][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.930][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.931][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.936][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.939][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.944][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.946][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.964][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:38.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:38.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:38.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:38.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:38.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:38.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:38.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:38.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:38.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.994][private$selectFields]
biodb.TRACE[2023-05-09 10:00:38.995][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:38.997][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:38.998][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:38.999][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.012][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.019][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.020][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.022][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.027][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.028][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:39.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.047][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-09 10:00:39.048][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:39.050][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:39.061][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:39.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:39.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:00:39.068][biodb::testThat]
biodb.INFO [2023-05-09 10:00:39.070][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-05-09 10:00:39.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:39.072][biodb::testThat]
biodb.TRACE[2023-05-09 10:00:39.077][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:00:39.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:00:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:39.187][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:39.191][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:39.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-09 10:00:39.195][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:39.197][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-09 10:00:39.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:39.238][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:39.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-09 10:00:39.242][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:39.244][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-09 10:00:39.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:39.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:39.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-09 10:00:39.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:39.321][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-09 10:00:39.326][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:39.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.361][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.363][private$selectFields]
biodb.TRACE[2023-05-09 10:00:39.364][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:39.366][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:39.367][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.369][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.371][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.374][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.377][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.380][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.384][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.390][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.392][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:39.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.417][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-09 10:00:39.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.454][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.455][private$selectFields]
biodb.TRACE[2023-05-09 10:00:39.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:39.458][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:39.460][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.465][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.466][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.472][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.474][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.475][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:39.477][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.479][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.482][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.483][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:39.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.505][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:39.506][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:39.508][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:39.858][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:39.862][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:39.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-05-09 10:00:39.866][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:39.868][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-05-09 10:00:39.872][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:00:39.876][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:00:39.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-05-09 10:00:39.880][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:00:39.881][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-05-09 10:00:39.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:39.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:39.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:39.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:39.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:39.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:39.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:39.985][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:00:39.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:39.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:39.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:39.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:39.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:40.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:40.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:40.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.022][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.024][private$selectFields]
biodb.TRACE[2023-05-09 10:00:40.025][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:40.026][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:40.028][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.034][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.039][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.041][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.042][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.044][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.045][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.048][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.049][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:40.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-09 10:00:40.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:40.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:40.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:40.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:40.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:40.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:40.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:40.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.097][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.099][private$selectFields]
biodb.TRACE[2023-05-09 10:00:40.100][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:40.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:40.103][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.109][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.114][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.116][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.117][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.123][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.124][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:40.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.143][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-09 10:00:40.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:40.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:40.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:40.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:40.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:40.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:40.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:00:40.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.173][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.174][private$selectFields]
biodb.TRACE[2023-05-09 10:00:40.175][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:00:40.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:00:40.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.181][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.184][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.188][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.190][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.191][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.193][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-09 10:00:40.194][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.195][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.198][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.200][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-09 10:00:40.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:40.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:40.219][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-09 10:00:40.221][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:00:40.222][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:00:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:40.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:40.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:00:40.266][biodb::testThat]
biodb.INFO [2023-05-09 10:00:40.267][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-05-09 10:00:40.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:40.270][biodb::testThat]
biodb.DEBUG[2023-05-09 10:00:40.273][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-09 10:00:40.274][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 10:00:40.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-09 10:00:40.278][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 10:00:40.280][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:00:40.282][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:00:40.283][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:00:40.285][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:00:40.286][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:00:40.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:40.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:40.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:40.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:40.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:40.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:40.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:40.306][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-05-09 10:00:40.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:40.311][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:40.313][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-05-09 10:00:42.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-05-09 10:00:44.341][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:44.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-05-09 10:00:44.365][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-05-09 10:00:44.379][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-05-09 10:00:44.385][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:00:44.408][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 10:00:44.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 10:00:44.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:44.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:44.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:44.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:44.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:44.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:44.427][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[2023-05-09 10:00:44.430][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.434][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.445][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:00:44.447][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:00:44.448][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.449][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.451][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:00:44.453][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:00:44.454][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.455][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.457][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:00:44.459][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:00:44.460][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.462][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.464][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:00:44.465][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:00:44.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.479][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.481][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:00:44.482][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:00:44.484][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.485][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.487][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:00:44.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:44.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.491][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.492][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:44.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:44.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.497][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.498][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:00:44.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:00:44.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.503][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.505][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:00:44.506][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:00:44.508][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.509][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.511][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:00:44.512][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:00:44.514][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.515][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:00:44.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:44.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:00:44.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:00:44.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:44.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:44.578][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-05-09 10:00:44.579][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-09 10:00:44.588][biodb::testThat]
biodb.INFO [2023-05-09 10:00:44.589][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-09 10:00:44.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:44.592][biodb::testThat]
biodb.DEBUG[2023-05-09 10:00:44.605][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-05-09 10:00:44.606][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-05-09 10:00:44.608][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-05-09 10:00:44.610][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-05-09 10:00:44.612][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-05-09 10:00:44.614][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:00:44.615][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:00:44.617][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:00:44.618][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:00:44.620][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:00:44.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:44.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:44.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:44.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:44.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:44.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:44.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:44.641][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-05-09 10:00:44.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:44.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:44.649][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-05-09 10:00:47.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-05-09 10:00:48.984][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:48.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-05-09 10:00:49.028][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-05-09 10:00:49.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:49.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:49.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:49.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:49.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:49.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:49.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:49.052][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-05-09 10:00:49.056][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:49.057][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:49.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-05-09 10:00:56.874][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-05-09 10:00:59.410][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:59.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-05-09 10:00:59.435][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-05-09 10:00:59.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:59.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:59.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:59.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:59.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:59.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:59.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:59.458][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-05-09 10:00:59.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:59.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:59.466][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-05-09 10:01:03.194][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-05-09 10:01:06.503][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:06.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-05-09 10:01:06.527][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-05-09 10:01:06.555][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-05-09 10:01:06.561][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:01:06.587][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-05-09 10:01:06.589][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-05-09 10:01:06.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:06.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:06.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:06.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:06.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:06.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:06.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:06.610][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.611][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.614][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.625][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:06.627][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:06.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.630][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.631][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:06.633][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:06.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.636][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:06.639][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:06.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.642][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.644][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.645][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.648][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.650][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.651][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.652][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.654][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.656][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:06.657][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:06.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.660][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.663][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.664][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.666][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.668][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:06.669][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:06.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.672][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.674][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:06.675][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:06.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.678][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:06.681][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:06.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.684][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:06.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:06.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:06.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:06.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:06.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:06.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:06.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:06.747][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.752][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.763][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:06.765][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:06.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.767][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.779][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:06.780][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:06.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.783][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.803][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:06.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:06.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.807][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:06.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.818][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.820][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.823][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:06.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.834][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.835][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.838][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.849][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:06.851][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:06.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.854][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.856][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:06.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:06.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.867][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.869][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:06.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.880][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:06.882][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:06.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.885][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:06.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:06.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.896][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:06.898][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:06.899][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.900][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:06.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:06.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:06.913][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:06.914][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.916][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:06.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:06.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:06.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:06.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:06.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:06.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:06.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:06.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:06.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:06.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:06.988][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.990][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.993][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:06.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:06.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.004][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:07.006][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:07.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.008][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:07.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:07.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.020][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:07.021][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:07.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.024][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:07.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:07.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.035][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:07.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:07.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.040][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:07.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.058][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:07.060][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:07.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.063][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:07.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:07.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.074][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:07.075][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:07.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.078][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.080][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.090][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:07.091][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:07.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.094][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:07.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:07.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:07.107][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:07.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.110][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:07.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:07.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.121][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:07.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:07.124][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.125][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:07.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:07.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:07.138][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:07.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.141][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:07.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:07.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.152][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:07.154][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:07.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.157][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:07.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:07.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:07.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:07.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:07.265][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-05-09 10:01:07.267][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-09 10:01:07.268][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-05-09 10:01:07.285][biodb::testThat]
biodb.INFO [2023-05-09 10:01:07.286][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-05-09 10:01:07.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:07.289][biodb::testThat]
biodb.INFO [2023-05-09 10:01:07.326][biodb::testThat]
biodb.INFO [2023-05-09 10:01:07.327][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-05-09 10:01:07.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:07.330][biodb::testThat]
biodb.INFO [2023-05-09 10:01:07.340][biodb::testThat]
biodb.INFO [2023-05-09 10:01:07.341][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-05-09 10:01:07.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:07.344][biodb::testThat]
biodb.DEBUG[2023-05-09 10:01:07.348][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:07.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:07.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:07.357][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:10.030][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:11.836][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:11.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-05-09 10:01:11.865][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-05-09 10:01:11.893][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:11.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:11.896][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:11.897][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:11.899][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:11.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:11.902][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:11.904][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 10:01:11.906][biodb::testThat]
biodb.INFO [2023-05-09 10:01:11.908][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-05-09 10:01:11.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:11.911][biodb::testThat]
biodb.ERROR[2023-05-09 10:01:11.932][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-05-09 10:01:11.957][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-05-09 10:01:11.990][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:01:11.992][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-09 10:01:11.994][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-09 10:01:11.995][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:01:11.997][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:11.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:11.999][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.002][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.003][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.INFO [2023-05-09 10:01:12.018][biodb::testContext]
biodb.INFO [2023-05-09 10:01:12.019][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:12.021][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-05-09 10:01:12.022][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:12.023][biodb::testContext]
biodb.INFO [2023-05-09 10:01:12.030][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:12.033][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:12.038][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:12.040][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 10:01:12.041][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.047][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 10:01:12.049][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.053][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[2023-05-09 10:01:12.054][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 10:01:12.056][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.062][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 10:01:12.063][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 10:01:12.065][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 10:01:12.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.070][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 10:01:12.072][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 10:01:12.074][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.079][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 10:01:12.081][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 10:01:12.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.085][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[2023-05-09 10:01:12.087][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 10:01:12.088][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 10:01:12.090][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 10:01:12.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.095][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 10:01:12.097][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.101][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[2023-05-09 10:01:12.103][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 10:01:12.104][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 10:01:12.106][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 10:01:12.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.111][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:12.113][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 10:01:12.114][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 10:01:12.116][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 10:01:12.117][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 10:01:12.119][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 10:01:12.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.124][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 10:01:12.125][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 10:01:12.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.131][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 10:01:12.132][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 10:01:12.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.138][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 10:01:12.139][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 10:01:12.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.145][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 10:01:12.146][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 10:01:12.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.151][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 10:01:12.153][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 10:01:12.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.158][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:12.160][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 10:01:12.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 10:01:12.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.168][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[2023-05-09 10:01:12.170][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 10:01:12.171][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 10:01:12.173][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 10:01:12.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.178][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 10:01:12.181][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.182][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-09 10:01:12.184][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:12.187][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.190][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.191][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.193][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:12.194][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:12.196][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.197][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 10:01:12.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:12.200][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.201][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.203][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:12.203][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:12.203][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:12.203][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:12.203][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:12.204][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:12.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:12.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.213][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.214][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:12.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:12.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.220][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.222][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 10:01:12.224][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.226][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:12.227][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:12.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.232][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.233][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.244][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:12.246][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:12.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.249][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 10:01:12.250][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:12.251][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.254][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:12.254][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:12.254][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:12.254][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:12.254][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:12.256][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:12.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:12.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.264][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.266][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:12.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:12.270][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.271][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.273][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 10:01:12.275][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.277][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-09 10:01:12.278][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:12.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.284][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.287][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:12.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:12.290][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.291][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 10:01:12.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:12.294][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.297][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:12.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:12.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.308][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.309][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:12.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:12.312][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.314][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.315][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 10:01:12.318][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.319][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:12.321][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.322][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:12.324][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.328][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.329][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:12.331][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:12.332][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.334][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 10:01:12.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:12.337][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.338][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.339][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.341][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:12.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:12.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.350][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.352][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:12.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:12.355][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.356][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:12.358][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:12.359][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.399][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.DEBUG[2023-05-09 10:01:12.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.412][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[2023-05-09 10:01:12.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.432][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[2023-05-09 10:01:12.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.464][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[2023-05-09 10:01:12.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.471][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 10:01:12.473][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 10:01:12.484][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 10:01:12.486][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 10:01:12.487][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:12.489][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 10:01:12.491][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:12.493][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:12.495][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 10:01:12.496][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 10:01:12.498][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:12.500][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 10:01:12.502][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:12.503][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:12.505][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 10:01:12.507][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:01:12.509][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 10:01:12.511][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 10:01:12.513][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:12.514][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 10:01:12.516][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 10:01:12.518][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 10:01:12.520][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 10:01:12.522][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 10:01:12.524][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 10:01:12.525][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 10:01:12.527][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 10:01:12.529][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 10:01:12.531][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 10:01:12.533][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 10:01:12.534][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 10:01:12.536][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 10:01:12.538][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 10:01:12.540][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 10:01:12.542][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 10:01:12.543][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 10:01:12.545][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 10:01:12.547][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 10:01:12.549][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 10:01:12.551][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 10:01:12.552][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 10:01:12.554][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 10:01:12.556][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 10:01:12.558][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 10:01:12.560][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 10:01:12.561][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 10:01:12.563][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 10:01:12.565][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 10:01:12.567][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 10:01:12.569][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 10:01:12.570][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 10:01:12.572][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 10:01:12.574][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 10:01:12.576][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 10:01:12.577][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 10:01:12.579][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 10:01:12.581][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 10:01:12.583][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 10:01:12.585][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 10:01:12.586][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 10:01:12.588][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 10:01:12.590][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 10:01:12.592][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 10:01:12.594][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 10:01:12.596][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 10:01:12.597][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 10:01:12.599][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:12.601][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:12.603][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 10:01:12.605][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 10:01:12.606][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 10:01:12.608][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 10:01:12.610][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 10:01:12.612][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 10:01:12.614][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 10:01:12.615][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 10:01:12.617][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 10:01:12.619][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 10:01:12.621][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 10:01:12.623][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 10:01:12.625][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 10:01:12.627][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 10:01:12.629][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 10:01:12.631][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 10:01:12.633][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:12.634][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:12.635][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.638][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.680][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[2023-05-09 10:01:12.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.722][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[2023-05-09 10:01:12.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.730][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.DEBUG[2023-05-09 10:01:12.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.747][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[2023-05-09 10:01:12.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:12.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:12.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:12.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:12.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:12.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:12.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:12.787][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.DEBUG[2023-05-09 10:01:12.789][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:12.791][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-09 10:01:12.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.795][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:12.799][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.800][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.801][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.802][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-09 10:01:12.804][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-09 10:01:12.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:12.806][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.807][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-09 10:01:12.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-09 10:01:12.810][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-09 10:01:12.811][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:12.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:12.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:12.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:12.814][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-09 10:01:12.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.818][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:12.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:12.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:12.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:12.822][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:01:12.822][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-09 10:01:12.824][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:12.825][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:12.826][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:12.827][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-09 10:01:12.827][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-09 10:01:12.829][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:12.831][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:12.833][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-09 10:01:12.835][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:12.837][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:12.839][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:12.844][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-09 10:01:12.845][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-09 10:01:12.847][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-09 10:01:12.849][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-09 10:01:12.850][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:12.852][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:12.853][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-09 10:01:12.855][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-09 10:01:12.856][biodb::testThat]
biodb.INFO [2023-05-09 10:01:12.858][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2023-05-09 10:01:12.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:12.860][biodb::testThat]
biodb.DEBUG[2023-05-09 10:01:12.865][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-09 10:01:12.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:12.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:12.873][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-05-09 10:01:14.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-05-09 10:01:16.141][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:16.151][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-05-09 10:01:16.165][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-05-09 10:01:16.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:16.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:16.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:16.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:19.985][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:21.946][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:21.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-05-09 10:01:21.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-05-09 10:01:21.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:21.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:21.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:21.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:21.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:21.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:21.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:21.994][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:21.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:22.001][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:22.003][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:23.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:24.518][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:24.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-05-09 10:01:24.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-05-09 10:01:24.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.615][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:24.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:24.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-05-09 10:01:24.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:24.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-05-09 10:01:24.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:24.647][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:24.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-05-09 10:01:24.651][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:24.653][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-05-09 10:01:24.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.685][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[2023-05-09 10:01:24.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:24.696][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:24.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-05-09 10:01:24.700][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:24.702][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-05-09 10:01:24.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:24.728][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:24.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-05-09 10:01:24.731][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:24.733][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-05-09 10:01:24.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:24.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:24.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:24.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:24.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:24.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:24.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:24.751][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:24.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:24.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:24.767][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:28.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:30.045][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:30.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-05-09 10:01:30.076][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-05-09 10:01:30.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:30.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:30.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:30.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:30.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:30.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:30.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-09 10:01:30.104][biodb::testThat]
biodb.INFO [2023-05-09 10:01:30.105][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2023-05-09 10:01:30.106][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:30.108][biodb::testThat]
biodb.DEBUG[2023-05-09 10:01:30.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:30.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:30.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:30.122][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:33.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:34.994][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:35.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-05-09 10:01:35.020][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-05-09 10:01:35.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:35.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:35.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:35.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:35.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:35.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:35.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:35.064][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:35.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:35.071][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:35.073][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:37.423][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:43.919][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:43.930][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-05-09 10:01:43.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-05-09 10:01:43.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:43.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:43.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:43.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:43.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:43.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:43.963][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.INFO [2023-05-09 10:01:43.966][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:01:43.968][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-09 10:01:43.969][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-09 10:01:43.970][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:01:43.971][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:43.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:43.974][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:43.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:43.977][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:43.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-09 10:01:43.984][biodb::testContext]
biodb.INFO [2023-05-09 10:01:43.985][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:43.986][biodb::testContext] Test context - Test web services
biodb.INFO [2023-05-09 10:01:43.987][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:43.989][biodb::testContext]
biodb.INFO [2023-05-09 10:01:43.995][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:43.998][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:44.002][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:44.004][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 10:01:44.005][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.009][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 10:01:44.011][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.022][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 10:01:44.024][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.031][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 10:01:44.033][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 10:01:44.035][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 10:01:44.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.040][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[2023-05-09 10:01:44.041][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 10:01:44.044][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 10:01:44.045][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.052][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 10:01:44.053][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 10:01:44.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.057][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[2023-05-09 10:01:44.059][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 10:01:44.061][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 10:01:44.062][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 10:01:44.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.068][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 10:01:44.070][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.075][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 10:01:44.077][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 10:01:44.079][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 10:01:44.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.085][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:44.086][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 10:01:44.088][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 10:01:44.090][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 10:01:44.135][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 10:01:44.137][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 10:01:44.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.141][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[2023-05-09 10:01:44.143][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 10:01:44.144][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 10:01:44.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.150][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 10:01:44.152][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 10:01:44.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.157][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 10:01:44.159][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 10:01:44.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.164][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 10:01:44.166][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 10:01:44.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.172][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 10:01:44.173][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 10:01:44.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.179][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:44.181][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 10:01:44.186][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 10:01:44.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.190][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[2023-05-09 10:01:44.192][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 10:01:44.193][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 10:01:44.195][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 10:01:44.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.201][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 10:01:44.204][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.206][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-09 10:01:44.208][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.209][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:44.211][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.212][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.217][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:44.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:44.220][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.222][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 10:01:44.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:44.225][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.228][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:44.228][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:44.228][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:44.228][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:44.228][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:44.230][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:44.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:44.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.239][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.240][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.242][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:44.243][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:44.245][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.246][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.248][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 10:01:44.251][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.252][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:44.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:44.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.263][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:44.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:44.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.268][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 10:01:44.269][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:44.271][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.274][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:44.274][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:44.274][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:44.274][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:44.274][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:44.275][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:44.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.280][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:44.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.286][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:44.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:44.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.292][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.294][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 10:01:44.297][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.298][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-09 10:01:44.300][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.301][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:44.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.305][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.309][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:44.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:44.313][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.315][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 10:01:44.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:44.319][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.323][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.324][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:44.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.329][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:44.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.333][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.334][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:44.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:44.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.340][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.342][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 10:01:44.345][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.346][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:44.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:44.350][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.352][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.353][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.355][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.356][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:44.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:44.359][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.361][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 10:01:44.362][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:44.364][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.365][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.367][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.368][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:44.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.372][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:44.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.377][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.378][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.380][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:44.381][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:44.382][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.384][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:44.394][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:44.395][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.476][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[2023-05-09 10:01:44.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.509][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 10:01:44.511][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 10:01:44.513][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 10:01:44.515][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 10:01:44.517][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:44.519][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 10:01:44.522][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:44.524][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:44.526][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 10:01:44.528][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 10:01:44.530][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:44.532][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 10:01:44.534][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:44.536][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:44.538][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 10:01:44.540][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:01:44.542][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 10:01:44.544][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 10:01:44.546][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:44.548][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 10:01:44.550][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 10:01:44.552][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 10:01:44.554][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 10:01:44.556][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 10:01:44.558][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 10:01:44.560][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 10:01:44.562][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 10:01:44.565][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 10:01:44.567][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 10:01:44.569][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 10:01:44.571][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 10:01:44.573][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 10:01:44.575][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 10:01:44.577][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 10:01:44.579][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 10:01:44.581][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 10:01:44.583][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 10:01:44.585][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 10:01:44.587][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 10:01:44.589][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 10:01:44.591][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 10:01:44.594][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 10:01:44.596][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 10:01:44.598][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 10:01:44.600][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 10:01:44.602][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 10:01:44.604][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 10:01:44.606][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 10:01:44.608][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 10:01:44.610][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 10:01:44.612][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 10:01:44.614][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 10:01:44.616][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 10:01:44.618][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 10:01:44.628][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 10:01:44.630][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 10:01:44.632][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 10:01:44.634][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 10:01:44.637][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 10:01:44.639][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 10:01:44.641][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 10:01:44.643][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 10:01:44.645][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 10:01:44.647][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 10:01:44.649][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 10:01:44.651][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 10:01:44.653][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:44.655][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:44.657][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 10:01:44.659][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 10:01:44.661][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 10:01:44.663][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 10:01:44.666][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 10:01:44.668][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 10:01:44.670][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 10:01:44.672][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 10:01:44.674][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 10:01:44.676][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 10:01:44.678][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 10:01:44.680][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 10:01:44.682][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 10:01:44.685][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 10:01:44.687][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 10:01:44.689][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 10:01:44.691][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:44.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:44.694][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.698][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.DEBUG[2023-05-09 10:01:44.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.717][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[2023-05-09 10:01:44.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.726][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[2023-05-09 10:01:44.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.735][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[2023-05-09 10:01:44.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.798][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[2023-05-09 10:01:44.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:44.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:44.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:44.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:44.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:44.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:44.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:44.853][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.DEBUG[2023-05-09 10:01:44.864][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:44.866][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-09 10:01:44.869][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.870][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:44.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.877][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.879][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-09 10:01:44.880][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-09 10:01:44.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:44.883][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.885][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-09 10:01:44.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-09 10:01:44.888][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-09 10:01:44.889][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:44.891][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:44.891][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:44.891][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:44.892][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-09 10:01:44.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.896][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:44.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:44.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:44.901][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:44.902][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:01:44.902][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-09 10:01:44.904][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:44.905][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:44.906][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:44.908][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-09 10:01:44.908][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-09 10:01:44.910][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:44.912][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:44.915][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-09 10:01:44.917][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:44.919][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:44.921][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:44.926][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-09 10:01:44.928][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-09 10:01:44.930][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-09 10:01:44.932][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-09 10:01:44.934][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:44.935][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:44.937][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-09 10:01:44.939][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-09 10:01:44.941][biodb::testThat]
biodb.INFO [2023-05-09 10:01:44.942][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-05-09 10:01:44.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:44.945][biodb::testThat]
biodb.DEBUG[2023-05-09 10:01:44.951][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-09 10:01:44.956][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:44.958][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-09 10:01:44.960][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:44.962][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-09 10:01:44.967][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:44.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:44.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:44.976][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-09 10:01:48.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-09 10:01:51.333][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:51.345][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-05-09 10:01:51.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-05-09 10:01:51.379][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:01:51.381][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-09 10:01:51.382][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-09 10:01:51.384][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:01:51.385][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:51.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:51.388][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.391][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-09 10:01:51.399][biodb::testContext]
biodb.INFO [2023-05-09 10:01:51.401][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:51.402][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-05-09 10:01:51.404][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:01:51.405][biodb::testContext]
biodb.INFO [2023-05-09 10:01:51.447][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:51.456][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:51.462][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:51.463][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 10:01:51.465][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.470][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 10:01:51.472][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.481][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 10:01:51.482][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.489][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 10:01:51.490][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 10:01:51.492][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 10:01:51.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.497][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 10:01:51.499][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 10:01:51.500][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.506][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 10:01:51.507][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 10:01:51.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.512][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 10:01:51.514][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 10:01:51.515][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 10:01:51.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.519][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[2023-05-09 10:01:51.520][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 10:01:51.522][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.527][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 10:01:51.528][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 10:01:51.529][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 10:01:51.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.535][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:51.536][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 10:01:51.537][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 10:01:51.539][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 10:01:51.540][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 10:01:51.542][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 10:01:51.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.547][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 10:01:51.549][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 10:01:51.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.553][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[2023-05-09 10:01:51.555][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 10:01:51.556][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 10:01:51.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.563][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 10:01:51.565][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 10:01:51.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.571][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 10:01:51.572][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 10:01:51.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.578][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 10:01:51.579][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 10:01:51.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.585][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:01:51.586][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 10:01:51.591][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 10:01:51.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.597][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 10:01:51.598][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 10:01:51.600][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 10:01:51.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.606][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 10:01:51.609][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.610][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-09 10:01:51.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.613][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:51.614][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.619][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:51.621][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:51.623][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.624][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 10:01:51.625][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:51.627][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.628][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.630][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:51.630][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:51.630][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:51.630][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:51.630][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:51.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:51.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:51.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.641][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:51.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:51.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.646][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.648][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 10:01:51.651][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.653][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:51.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:51.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.661][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.662][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:51.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:51.665][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.666][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 10:01:51.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:51.669][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.672][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:51.672][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:51.672][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:51.672][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:01:51.672][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:01:51.673][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:51.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:51.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.682][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:51.684][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:51.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.687][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.689][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 10:01:51.691][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-09 10:01:51.694][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:51.696][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.699][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.700][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.710][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:01:51.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:51.713][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.715][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 10:01:51.716][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:51.718][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.719][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.720][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.722][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:51.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.725][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:51.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.730][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:51.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:51.734][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.735][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.737][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 10:01:51.739][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.740][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:01:51.742][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.743][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:51.744][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.746][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.747][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.749][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:01:51.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:51.752][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.753][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 10:01:51.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:51.756][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.757][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:51.758][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:01:51.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:51.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:51.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:51.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:51.768][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.769][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:51.770][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:51.771][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:51.772][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:01:51.774][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:51.775][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.787][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.DEBUG[2023-05-09 10:01:51.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.798][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[2023-05-09 10:01:51.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.821][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.DEBUG[2023-05-09 10:01:51.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.832][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.DEBUG[2023-05-09 10:01:51.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.861][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.DEBUG[2023-05-09 10:01:51.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.867][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[2023-05-09 10:01:51.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:51.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:51.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:51.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:51.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:51.874][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 10:01:51.876][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 10:01:51.878][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 10:01:51.880][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 10:01:51.882][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:51.883][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 10:01:51.885][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:51.887][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:51.889][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 10:01:51.891][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 10:01:51.893][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:51.894][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 10:01:51.896][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 10:01:51.898][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 10:01:51.900][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 10:01:51.902][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:01:51.904][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 10:01:51.906][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 10:01:51.908][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:51.909][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 10:01:51.911][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 10:01:51.913][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 10:01:51.915][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 10:01:51.925][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 10:01:51.927][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 10:01:51.929][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 10:01:51.932][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 10:01:51.934][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 10:01:51.936][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 10:01:51.938][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 10:01:51.939][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 10:01:51.941][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 10:01:51.943][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 10:01:51.945][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 10:01:51.947][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 10:01:51.949][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 10:01:51.950][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 10:01:51.952][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 10:01:51.954][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 10:01:51.956][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 10:01:51.958][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 10:01:51.959][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 10:01:51.961][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 10:01:51.963][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 10:01:51.965][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 10:01:51.967][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 10:01:51.968][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 10:01:51.970][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 10:01:51.972][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 10:01:51.974][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 10:01:51.976][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 10:01:51.977][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 10:01:51.979][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 10:01:51.981][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 10:01:51.983][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 10:01:51.985][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 10:01:51.987][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 10:01:51.989][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 10:01:51.991][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 10:01:51.993][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 10:01:51.995][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 10:01:51.997][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 10:01:51.999][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 10:01:52.004][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 10:01:52.014][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 10:01:52.016][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 10:01:52.019][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:52.021][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:52.023][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 10:01:52.025][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 10:01:52.027][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 10:01:52.030][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 10:01:52.032][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 10:01:52.034][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 10:01:52.036][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 10:01:52.038][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 10:01:52.040][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 10:01:52.043][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 10:01:52.045][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 10:01:52.047][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 10:01:52.049][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 10:01:52.051][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 10:01:52.054][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 10:01:52.057][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 10:01:52.060][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:01:52.062][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:01:52.064][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.066][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.255][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[2023-05-09 10:01:52.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:01:52.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.291][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-09 10:01:52.293][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-09 10:01:52.296][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:52.297][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 10:01:52.299][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:52.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:01:52.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:52.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:01:52.304][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:52.305][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-09 10:01:52.307][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-09 10:01:52.308][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:01:52.309][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:52.311][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-09 10:01:52.312][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-09 10:01:52.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-09 10:01:52.315][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 10:01:52.316][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:01:52.316][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:01:52.316][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:01:52.318][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-09 10:01:52.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:52.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:52.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:01:52.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:01:52.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:01:52.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:01:52.327][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:01:52.327][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-09 10:01:52.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:01:52.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:01:52.330][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 10:01:52.332][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-09 10:01:52.332][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-09 10:01:52.334][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:01:52.336][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:01:52.339][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-09 10:01:52.341][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:01:52.343][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:01:52.345][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:01:52.350][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-09 10:01:52.351][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-09 10:01:52.353][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-09 10:01:52.355][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-09 10:01:52.357][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:52.358][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-09 10:01:52.360][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-09 10:01:52.361][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-09 10:01:52.363][biodb::testThat]
biodb.INFO [2023-05-09 10:01:52.365][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-05-09 10:01:52.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:52.367][biodb::testThat]
biodb.DEBUG[2023-05-09 10:01:52.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-09 10:01:52.378][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:52.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-09 10:01:52.382][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:52.384][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-09 10:01:52.390][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-09 10:01:52.394][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:01:52.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-05-09 10:01:52.398][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:01:52.400][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-05-09 10:01:52.404][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-05-09 10:01:52.405][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 10:01:52.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-05-09 10:01:52.409][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 10:01:52.411][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:01:52.412][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:01:52.414][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-09 10:01:52.415][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:01:52.416][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:01:52.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:52.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:52.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:52.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:52.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:52.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:52.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:52.436][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-05-09 10:01:52.440][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:52.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:52.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-05-09 10:01:56.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-05-09 10:01:59.403][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:59.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-05-09 10:01:59.426][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-05-09 10:01:59.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-05-09 10:01:59.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:01:59.466][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-09 10:01:59.467][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-09 10:01:59.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:59.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:59.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:59.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:59.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:59.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:59.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:59.487][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.490][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.501][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:59.502][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:59.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.505][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-09 10:01:59.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-09 10:01:59.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.515][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:59.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:59.518][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.519][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:59.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.530][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-09 10:01:59.531][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-09 10:01:59.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.534][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.535][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-09 10:01:59.537][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-09 10:01:59.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.539][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:59.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:59.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.545][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:59.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:59.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.555][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:59.557][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:59.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.559][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-09 10:01:59.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.570][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:59.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:59.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.574][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.584][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:59.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:59.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.588][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:59.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:59.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.609][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:59.611][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:59.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.614][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.616][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-09 10:01:59.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-09 10:01:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.626][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:59.627][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:59.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.630][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-09 10:01:59.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-09 10:01:59.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:59.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:59.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:59.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:59.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:59.698][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-05-09 10:01:59.700][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:01:59.702][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-09 10:01:59.703][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-09 10:01:59.704][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:01:59.706][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:59.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:59.708][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:59.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:59.710][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:59.711][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 355 ]
> 
> proc.time()
   user  system elapsed 
 36.837   1.974 210.866

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.7840.2887.675
ChebiEntry0.5310.0290.560