Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 206/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: b5e26aa
git_last_commit_date: 2025-06-24 10:11:00 -0400 (Tue, 24 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

CHECK results for biodbChebi on nebbiolo2

To the developers/maintainers of the biodbChebi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbChebi
Version: 1.15.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings biodbChebi_1.15.1.tar.gz
StartedAt: 2025-08-31 20:43:50 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 20:45:00 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings biodbChebi_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.15.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.15.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-08-31 20:44:35.363][biodb::testContext]
biodb.INFO [2025-08-31 20:44:35.365][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:35.366][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-31 20:44:35.367][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:35.368][biodb::testContext]
biodb.INFO [2025-08-31 20:44:35.375][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:35.377][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:35.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:35.386][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-31 20:44:35.387][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.391][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-31 20:44:35.412][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.416][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-31 20:44:35.417][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.421][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-31 20:44:35.422][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-31 20:44:35.423][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-31 20:44:35.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.427][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-31 20:44:35.428][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-31 20:44:35.429][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.433][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-31 20:44:35.434][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-31 20:44:35.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.446][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[2025-08-31 20:44:35.447][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-31 20:44:35.448][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-31 20:44:35.449][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-31 20:44:35.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.452][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-31 20:44:35.453][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.456][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[2025-08-31 20:44:35.457][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-31 20:44:35.458][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-31 20:44:35.458][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-31 20:44:35.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.462][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:35.463][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-31 20:44:35.464][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-31 20:44:35.465][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-31 20:44:35.465][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-31 20:44:35.466][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-31 20:44:35.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.469][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[2025-08-31 20:44:35.470][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-31 20:44:35.471][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-31 20:44:35.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.474][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-31 20:44:35.475][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-31 20:44:35.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.478][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-31 20:44:35.479][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-31 20:44:35.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.483][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-31 20:44:35.484][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-31 20:44:35.485][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-31 20:44:35.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.487][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[2025-08-31 20:44:35.488][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:35.489][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-31 20:44:35.493][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-31 20:44:35.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.497][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-31 20:44:35.498][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-31 20:44:35.499][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-31 20:44:35.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.501][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[2025-08-31 20:44:35.505][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-31 20:44:35.536][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.552][self$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[2025-08-31 20:44:35.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:35.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.559][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:35.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:35.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.562][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-31 20:44:35.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:35.564][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:35.565][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:35.566][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:35.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:35.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.572][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.573][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.574][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:35.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:35.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.576][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.578][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-31 20:44:35.579][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.580][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:35.581][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:35.583][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.587][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:35.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:35.589][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.590][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-31 20:44:35.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:35.592][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.594][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:35.594][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:35.594][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:35.594][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:35.594][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:35.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:35.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:35.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.600][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.601][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.602][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:35.603][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:35.604][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.605][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.606][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-31 20:44:35.607][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.608][self$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[2025-08-31 20:44:35.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:35.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.615][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:35.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:35.617][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.618][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-31 20:44:35.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:35.620][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.621][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.621][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:35.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:35.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.629][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:35.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:35.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.632][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.633][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-31 20:44:35.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:35.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:35.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.641][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.642][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.643][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:35.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:35.645][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.646][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-31 20:44:35.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:35.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.653][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:35.654][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.655][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:35.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:35.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:35.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:35.660][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:35.661][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:35.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:35.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:35.665][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:35.668][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:35.669][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.683][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[2025-08-31 20:44:35.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.691][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[2025-08-31 20:44:35.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.708][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[2025-08-31 20:44:35.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.717][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[2025-08-31 20:44:35.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.726][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[2025-08-31 20:44:35.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.730][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[2025-08-31 20:44:35.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.739][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-31 20:44:35.744][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-31 20:44:35.745][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-31 20:44:35.747][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-31 20:44:35.748][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:35.749][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-31 20:44:35.751][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:35.752][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:35.754][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-31 20:44:35.755][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-31 20:44:35.756][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:35.758][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-31 20:44:35.759][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:35.760][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:35.762][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-31 20:44:35.763][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-31 20:44:35.764][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-31 20:44:35.766][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-31 20:44:35.767][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:35.769][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-31 20:44:35.770][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-31 20:44:35.771][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-31 20:44:35.773][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-31 20:44:35.774][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-31 20:44:35.775][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-31 20:44:35.777][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-31 20:44:35.778][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-31 20:44:35.779][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-31 20:44:35.781][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-31 20:44:35.782][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-31 20:44:35.783][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-31 20:44:35.785][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-31 20:44:35.786][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-31 20:44:35.787][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-31 20:44:35.789][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-31 20:44:35.790][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-31 20:44:35.791][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-31 20:44:35.793][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-31 20:44:35.794][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-31 20:44:35.795][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-31 20:44:35.797][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-31 20:44:35.798][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-31 20:44:35.799][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-31 20:44:35.801][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-31 20:44:35.802][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-31 20:44:35.803][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-31 20:44:35.805][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-31 20:44:35.806][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-31 20:44:35.807][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-31 20:44:35.809][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-31 20:44:35.810][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-31 20:44:35.811][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-31 20:44:35.813][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-31 20:44:35.819][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-31 20:44:35.822][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-31 20:44:35.824][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-31 20:44:35.825][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-31 20:44:35.827][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-31 20:44:35.829][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-31 20:44:35.830][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-31 20:44:35.832][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-31 20:44:35.833][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-31 20:44:35.835][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-31 20:44:35.836][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-31 20:44:35.838][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-31 20:44:35.839][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-31 20:44:35.841][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:35.842][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:35.844][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-31 20:44:35.845][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-31 20:44:35.847][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-31 20:44:35.848][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-31 20:44:35.850][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-31 20:44:35.851][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-31 20:44:35.853][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-31 20:44:35.854][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-31 20:44:35.856][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-31 20:44:35.857][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-31 20:44:35.859][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-31 20:44:35.860][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-31 20:44:35.862][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-31 20:44:35.863][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-31 20:44:35.865][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-31 20:44:35.887][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-31 20:44:35.889][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:35.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:35.894][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.896][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.908][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.DEBUG[2025-08-31 20:44:35.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.941][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.DEBUG[2025-08-31 20:44:35.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.967][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.DEBUG[2025-08-31 20:44:35.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.980][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.DEBUG[2025-08-31 20:44:35.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:35.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:35.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:35.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:35.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:35.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:35.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:35.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:36.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:36.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:36.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:36.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:36.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:36.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:36.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:36.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:36.008][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:36.018][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-31 20:44:36.021][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:36.022][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-31 20:44:36.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:36.024][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:36.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:36.026][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:36.027][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:36.028][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-31 20:44:36.029][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-31 20:44:36.030][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:36.031][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:36.032][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-31 20:44:36.033][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-31 20:44:36.034][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-31 20:44:36.035][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:36.036][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:36.036][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:36.036][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:36.037][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-31 20:44:36.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:36.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:36.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:36.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:36.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:36.043][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:36.044][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-31 20:44:36.044][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-31 20:44:36.045][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:36.046][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:36.047][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:36.048][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-31 20:44:36.048][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-31 20:44:36.054][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:36.056][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:36.058][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-31 20:44:36.059][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:36.061][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:36.062][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:36.085][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-31 20:44:36.103][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-31 20:44:36.113][biodb::testThat]
biodb.INFO [2025-08-31 20:44:36.114][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-31 20:44:36.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:36.116][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:36.130][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-31 20:44:36.132][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:36.135][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:36.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:36.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:36.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:36.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:36.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:36.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:36.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:36.170][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.172][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.173][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.191][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.194][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.220][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.224][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.225][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.227][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.233][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.234][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.236][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.241][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.242][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.244][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.249][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.250][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.252][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.258][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:36.259][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.261][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.267][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.268][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.270][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.276][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.277][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.285][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:36.286][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.288][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.289][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:36.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.294][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.295][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.297][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:36.377][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-31 20:44:36.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.424][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:36.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:36.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.427][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:36.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:36.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:36.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.435][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:36.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:36.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.520][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.521][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.523][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.547][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.548][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.550][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:36.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.573][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.599][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.602][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.602][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.625][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.626][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.627][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.652][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.660][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.676][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.680][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.684][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.685][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.687][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.699][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.707][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.711][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.712][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.727][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.731][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.735][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.740][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.741][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.743][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.744][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.759][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.763][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.767][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.797][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.823][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.826][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.873][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:36.875][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:36.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.876][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.881][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:36.882][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:36.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.884][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.888][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:36.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:36.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.891][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:36.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:36.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.898][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.902][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.903][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:36.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.905][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.909][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.910][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:36.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.911][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.916][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.917][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:36.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.918][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.923][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.924][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:36.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.925][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.929][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.930][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:36.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.932][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.936][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:36.937][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:36.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.939][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:36.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:36.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:36.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:36.946][ef$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:36.953][biodb::testThat]
biodb.INFO [2025-08-31 20:44:36.954][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-31 20:44:36.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:36.955][biodb::testThat]
biodb.DEBUG[2025-08-31 20:44:36.969][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-31 20:44:36.972][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:36.976][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:36.982][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml.
biodb.DEBUG[2025-08-31 20:44:36.983][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:37.006][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:37.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:37.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:37.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:37.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:37.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:37.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:37.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:37.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:37.020][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.021][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.023][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.048][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:37.050][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:37.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.051][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.053][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:37.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:37.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.057][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:37.058][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:37.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.059][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.061][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:37.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.064][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.065][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.067][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.072][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.073][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.075][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.080][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:37.081][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:37.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.083][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.084][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:37.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:37.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.088][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:37.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.092][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:37.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.096][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.104][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.107][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.113][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:37.114][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:37.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.115][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:37.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:37.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:37.122][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:37.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.123][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:37.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:37.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:37.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:37.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:37.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:37.167][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-31 20:44:37.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-31 20:44:37.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-31 20:44:37.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-31 20:44:37.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-31 20:44:37.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-31 20:44:37.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-31 20:44:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:37.185][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.186][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-31 20:44:37.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.188][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:37.191][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.194][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:37.195][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-31 20:44:37.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:37.238][function(conn, opt)] With value "squalene".
sched.DEBUG[2025-08-31 20:44:37.243][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-31 20:44:37.263][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:37.269][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-31 20:44:37.270][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:37.289][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".
fscache.INFO [2025-08-31 20:44:37.318][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:37.322][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:37.323][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:37.325][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-31 20:44:37.336][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.337][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:37.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.339][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.340][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.341][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.343][ef$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:37.347][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.348][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-31 20:44:37.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.349][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:37.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:37.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:37.445][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".
fscache.INFO [2025-08-31 20:44:37.448][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:37.452][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:37.453][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.INFO [2025-08-31 20:44:37.467][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.468][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-31 20:44:37.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.470][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.514][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:37.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:37.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:37.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:37.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:37.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:37.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:37.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.577][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.581][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-31 20:44:37.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.584][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:37.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-31 20:44:37.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:37.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:37.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-31 20:44:37.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:37.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:37.598][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.599][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-31 20:44:37.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.601][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.608][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.609][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-31 20:44:37.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.611][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.618][biodb::testThat]
biodb.INFO [2025-08-31 20:44:37.619][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-31 20:44:37.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:37.621][biodb::testThat]
biodb.DEBUG[2025-08-31 20:44:37.624][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
sched.TRACE[2025-08-31 20:44:38.344][try_get_rcurl_content] Using RCurl package for sending request (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440).
biodb.INFO [2025-08-31 20:44:39.592][biodb::testThat]
biodb.INFO [2025-08-31 20:44:39.593][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-31 20:44:39.595][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:39.596][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:39.603][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:39.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:39.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.607][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.608][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:39.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:39.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.611][ef$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:39.613][biodb::testThat]
biodb.INFO [2025-08-31 20:44:39.614][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-08-31 20:44:39.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:39.616][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:39.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:39.761][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".
fscache.INFO [2025-08-31 20:44:39.764][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:39.768][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:39.769][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:39.873][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".
fscache.INFO [2025-08-31 20:44:39.876][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:39.880][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:39.881][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.TRACE[2025-08-31 20:44:39.896][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-31 20:44:39.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-31 20:44:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:39.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:39.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:39.934][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".
fscache.INFO [2025-08-31 20:44:39.937][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:39.940][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-31 20:44:39.941][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:39.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:39.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:39.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:39.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:39.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:39.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:39.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:39.955][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-31 20:44:40.004][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:40.006][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:40.010][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml.
biodb.DEBUG[2025-08-31 20:44:40.011][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.012][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:40.014][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:40.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.028][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.029][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.031][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.044][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.047][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.049][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.053][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.054][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.056][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.062][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.063][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.065][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.072][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.080][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.081][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.083][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.085][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.086][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.089][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.097][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.102][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.105][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.111][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.112][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.116][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.120][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.121][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.123][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.171][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-31 20:44:40.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:40.196][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:40.199][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:40.202][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-31 20:44:40.203][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:40.263][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-31 20:44:40.264][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:40.266][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:40.270][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml.
biodb.DEBUG[2025-08-31 20:44:40.271][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:40.274][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:40.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.289][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.298][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.300][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.302][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.303][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.308][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.311][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.317][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.318][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.320][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.326][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.327][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.336][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.338][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.339][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.340][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.344][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.351][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.357][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.360][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.367][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.369][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.375][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.376][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.378][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.433][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-31 20:44:40.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:40.466][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".
fscache.INFO [2025-08-31 20:44:40.469][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:40.473][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:40.474][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.488][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[2025-08-31 20:44:40.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:40.514][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-31 20:44:40.515][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:40.517][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:40.520][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml.
biodb.DEBUG[2025-08-31 20:44:40.521][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.522][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:40.523][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:40.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.539][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.542][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.548][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.551][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.555][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.557][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.558][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.560][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.561][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.563][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.565][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.566][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.567][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.578][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.579][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.585][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.586][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.588][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.589][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.595][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.596][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.598][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.599][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.604][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.605][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.607][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.651][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-31 20:44:40.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:40.685][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-31 20:44:40.686][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:40.688][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:40.692][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml.
biodb.DEBUG[2025-08-31 20:44:40.693][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.695][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:40.696][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:40.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.710][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.711][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.713][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.719][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.720][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.724][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.727][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.729][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.730][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.732][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.733][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.735][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.738][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.739][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.741][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.743][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.744][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.746][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.755][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.758][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.760][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.761][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.769][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.770][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.772][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.774][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.778][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.779][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.781][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.826][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-31 20:44:40.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:40.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.861][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[2025-08-31 20:44:40.863][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-31 20:44:40.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:40.866][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:40.870][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml.
biodb.DEBUG[2025-08-31 20:44:40.871][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:40.873][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:40.874][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:40.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:40.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:40.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:40.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:40.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:40.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:40.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:40.890][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.893][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.900][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:40.901][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:40.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.903][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.904][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:40.906][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:40.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.908][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:40.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:40.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.913][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.914][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.915][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:40.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.917][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.919][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.920][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:40.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.922][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.924][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:40.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:40.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.927][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.929][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.930][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:40.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.932][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.942][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.945][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:40.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:40.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.953][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.954][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.956][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.958][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:40.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.963][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:40.964][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:40.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.966][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:40.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:40.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.011][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-31 20:44:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:41.046][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-31 20:44:41.047][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:41.049][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:41.055][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml.
biodb.DEBUG[2025-08-31 20:44:41.056][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:41.057][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:41.058][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:41.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:41.073][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.075][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.077][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.083][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.084][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.086][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.092][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.096][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.102][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.103][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.105][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.111][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.112][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.131][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.133][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.137][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.138][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.140][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.141][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.149][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.155][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.156][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.158][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.165][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.167][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.178][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.227][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-31 20:44:41.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:41.253][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-31 20:44:41.254][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:41.256][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:41.261][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml.
biodb.DEBUG[2025-08-31 20:44:41.262][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:41.264][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:41.265][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:41.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.279][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[2025-08-31 20:44:41.282][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.285][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.291][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.292][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.294][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.296][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.301][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.302][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.304][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.318][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.319][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.321][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.330][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.338][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.344][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.345][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.348][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.357][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.363][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.373][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.377][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.381][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.382][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.433][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-31 20:44:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:41.459][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-31 20:44:41.460][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:41.462][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:41.466][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml.
biodb.DEBUG[2025-08-31 20:44:41.467][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:41.469][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:41.470][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:41.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:41.493][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.497][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.502][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.504][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.506][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.512][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.513][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.515][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.521][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.522][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.524][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.530][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.531][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.533][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.540][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.541][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.543][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.544][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.546][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.548][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.549][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.554][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.555][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.557][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.563][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.566][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.573][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.574][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.582][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.586][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.587][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.636][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-31 20:44:41.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:41.663][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-31 20:44:41.664][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:41.674][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:41.680][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml.
biodb.DEBUG[2025-08-31 20:44:41.681][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:41.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:41.684][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:41.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.697][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[2025-08-31 20:44:41.699][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.703][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.708][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.709][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.711][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.713][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.718][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.719][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.721][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.727][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.728][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.739][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.746][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.748][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.750][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.753][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.771][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.777][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.778][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.780][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.785][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.787][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.790][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.837][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-31 20:44:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:41.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:41.869][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-31 20:44:41.870][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:41.872][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:41.876][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml.
biodb.DEBUG[2025-08-31 20:44:41.877][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:41.878][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:41.880][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:41.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:41.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:41.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:41.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:41.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:41.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:41.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:41.895][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.898][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:41.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.904][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.905][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.907][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.909][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:41.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:41.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.913][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.915][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.917][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:41.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.922][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.925][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:41.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:41.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.943][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.944][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.949][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:41.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:41.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.957][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:41.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.962][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.965][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:41.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:41.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.971][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.974][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.976][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:41.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.980][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.981][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:41.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:41.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:41.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:41.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:41.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:41.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.039][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-31 20:44:42.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:42.063][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-31 20:44:42.065][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.066][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.070][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml.
biodb.DEBUG[2025-08-31 20:44:42.072][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:42.073][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:42.074][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:42.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:42.089][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.090][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.092][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.098][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.099][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.101][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.102][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.106][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.108][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.110][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.118][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.124][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.133][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.134][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.136][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.138][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.139][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.142][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.147][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.148][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.150][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.155][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.156][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.158][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.165][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.167][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.178][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.230][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-31 20:44:42.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:42.256][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-31 20:44:42.257][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.259][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.263][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml.
biodb.DEBUG[2025-08-31 20:44:42.264][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:42.265][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:42.266][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:42.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:42.279][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.282][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.288][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.290][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.292][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.296][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.298][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.306][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.315][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.320][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.321][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.324][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.325][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.327][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.328][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.332][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.333][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.335][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.340][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.343][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.349][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.350][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.352][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.353][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.357][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.358][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.360][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.419][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-31 20:44:42.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.445][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[2025-08-31 20:44:42.446][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-31 20:44:42.448][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.449][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.453][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml.
biodb.DEBUG[2025-08-31 20:44:42.454][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:42.455][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:42.457][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:42.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.469][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.TRACE[2025-08-31 20:44:42.472][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.476][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.481][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.482][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.484][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.486][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.490][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.491][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.493][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.499][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.500][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.502][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.503][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.505][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.508][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.509][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.513][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.514][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.516][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.517][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.521][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.523][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.525][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.530][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.532][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.534][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.540][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.541][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.543][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.544][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.586][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.629][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-31 20:44:42.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:42.652][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-31 20:44:42.653][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.654][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.657][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml.
biodb.DEBUG[2025-08-31 20:44:42.658][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:42.659][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:42.660][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:42.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:42.673][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.674][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.676][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.681][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.682][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.684][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.685][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.689][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.692][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.700][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.701][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.704][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.705][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.706][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.708][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.710][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.711][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.712][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.720][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.726][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.727][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.728][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.734][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.735][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.741][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.743][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.747][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.748][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.750][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.790][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-31 20:44:42.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:42.812][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-31 20:44:42.813][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.814][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.818][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml.
biodb.DEBUG[2025-08-31 20:44:42.819][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:42.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:42.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:42.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:42.834][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.837][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.843][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.846][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:42.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:42.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.851][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.854][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:42.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:42.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.859][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.862][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:42.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:42.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.868][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.869][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.871][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.876][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:42.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.879][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.880][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.882][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.883][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.889][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.890][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.892][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:42.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.902][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.906][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:42.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:42.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.912][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.913][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.916][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:42.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:42.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.920][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.921][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.924][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:42.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:42.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:42.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:42.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:42.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.968][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-31 20:44:42.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:42.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:42.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:42.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:42.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:42.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:42.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:42.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:42.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:42.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:42.991][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-31 20:44:42.992][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:42.993][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:42.998][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml.
biodb.DEBUG[2025-08-31 20:44:42.999][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.000][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.001][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.014][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.017][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.023][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.024][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.027][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.031][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.032][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.034][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.039][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.040][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.048][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.049][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.050][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.056][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.057][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.058][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.060][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.061][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.067][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.069][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.076][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.084][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.089][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.090][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.092][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.097][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.098][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.100][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.101][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.143][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-31 20:44:43.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:43.166][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-31 20:44:43.167][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:43.168][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:43.173][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml.
biodb.DEBUG[2025-08-31 20:44:43.174][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.175][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.176][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.189][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.190][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.192][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.197][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.198][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.200][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.205][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.206][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.213][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.214][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.216][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.225][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.227][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.228][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.233][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.234][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.236][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.237][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.238][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.240][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.253][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.256][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.264][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.269][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.270][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.272][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.316][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-31 20:44:43.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:43.340][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-31 20:44:43.341][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:43.342][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:43.347][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml.
biodb.DEBUG[2025-08-31 20:44:43.348][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.349][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.350][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.364][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.365][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.367][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.372][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.373][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.387][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.388][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.391][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.397][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.399][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.408][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.413][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.414][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.416][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.417][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.418][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.420][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.421][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.426][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.434][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.437][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.442][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.443][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.445][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.447][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.452][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.454][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.455][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.497][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-31 20:44:43.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:43.521][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-31 20:44:43.522][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:43.523][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:43.528][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml.
biodb.DEBUG[2025-08-31 20:44:43.529][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.530][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.531][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.545][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.554][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.560][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.561][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.563][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.568][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.569][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.571][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.577][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.579][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.593][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.594][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.596][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.597][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.600][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.607][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.608][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.614][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.615][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.617][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.622][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.623][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.625][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.631][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.632][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.633][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.678][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-31 20:44:43.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:43.700][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-31 20:44:43.701][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:43.703][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:43.706][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml.
biodb.DEBUG[2025-08-31 20:44:43.712][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.713][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.714][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.727][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.735][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.736][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.738][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.743][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.744][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.746][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.751][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.752][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.754][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.760][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.767][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.768][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.771][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.772][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.774][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.775][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.782][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.787][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.788][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.795][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.796][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.798][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:43.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:43.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.803][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.804][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.806][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:43.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:43.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.860][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-31 20:44:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:43.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.903][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[2025-08-31 20:44:43.904][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-31 20:44:43.905][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:43.907][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:43.911][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml.
biodb.DEBUG[2025-08-31 20:44:43.912][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:43.913][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:43.915][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:43.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:43.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:43.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:43.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:43.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:43.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:43.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:43.929][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.932][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:43.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:43.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.938][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.941][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.943][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:43.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:43.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.947][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.950][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:43.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.956][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.957][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.959][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:43.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.965][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.966][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.968][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:43.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.974][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.975][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:43.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.978][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.979][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.981][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.987][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.988][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.990][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:43.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:43.995][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:43.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:43.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:43.998][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:44.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:44.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.004][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.005][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.007][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.008][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.012][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.015][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.065][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-31 20:44:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:44.094][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:44.096][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:44.100][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:44.101][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:44.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:44.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:44.651][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:44.653][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/63dc67d905e130c19900bd338bad7ba9.content.
sched.DEBUG[2025-08-31 20:44:44.654][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:44.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:44.660][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:44.663][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/287cac4c6e727656d926f26e3952924c.content.
sched.DEBUG[2025-08-31 20:44:44.664][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:44.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:44.677][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-31 20:44:44.678][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:44.680][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:44.684][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml.
biodb.DEBUG[2025-08-31 20:44:44.685][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:44.687][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:44.688][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:44.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.707][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.716][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:44.717][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:44.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.719][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.720][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:44.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:44.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.724][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:44.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:44.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.727][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:44.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:44.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:44.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:44.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:44.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:44.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.741][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.744][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.749][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.750][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.752][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.754][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.758][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:44.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.761][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.769][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.775][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:44.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:44.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.778][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:44.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:44.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.783][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.785][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.786][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.792][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.793][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.795][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.796][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:44.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.840][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-31 20:44:44.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:44.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:44.891][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-31 20:44:44.892][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:44.894][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:44.897][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml.
biodb.DEBUG[2025-08-31 20:44:44.898][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:44.900][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:44.901][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:44.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:44.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:44.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:44.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:44.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:44.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:44.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:44.914][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.915][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.917][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:44.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:44.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.922][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:44.923][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:44.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.925][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.926][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:44.931][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:44.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.933][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:44.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:44.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.938][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:44.939][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:44.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.941][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:44.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.949][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:44.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.956][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:44.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.958][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.959][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:44.960][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.962][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.963][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:44.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:44.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.970][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:44.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.975][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:44.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:44.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:44.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:44.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.983][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.984][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.986][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.988][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:44.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:44.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.992][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.993][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.994][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.996][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:44.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:44.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:44.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:45.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:45.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:45.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.043][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-31 20:44:45.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:45.072][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:45.074][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:45.078][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:45.079][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:45.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:45.590][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:45.593][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:45.596][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-31 20:44:45.598][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:45.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:45.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:45.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:45.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:45.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:45.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:45.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:45.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:45.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:46.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:46.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:46.132][biodb::testThat]
biodb.INFO [2025-08-31 20:44:46.133][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-31 20:44:46.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:46.135][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:46.137][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-31 20:44:46.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-31 20:44:46.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:46.177][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.180][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.182][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-31 20:44:46.183][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:46.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:46.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.211][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.213][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-31 20:44:46.214][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:46.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.260][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:46.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.280][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.281][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.282][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.288][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.294][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.295][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.296][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.298][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.299][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.330][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-31 20:44:46.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.352][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.353][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.354][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.355][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.360][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.361][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.364][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.366][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.366][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.368][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.369][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.370][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.384][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:46.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.403][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.404][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.405][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.406][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.409][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.411][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.413][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.415][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.417][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.422][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.436][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-31 20:44:46.437][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:46.438][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:46.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:46.542][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.545][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.547][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-31 20:44:46.548][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:46.551][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.553][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.556][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-31 20:44:46.557][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:46.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:46.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.658][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:46.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.700][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.701][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.702][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.703][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.704][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.705][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.706][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.708][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.712][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.713][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.714][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.718][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.719][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.732][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-31 20:44:46.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.791][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.792][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.793][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.794][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.800][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.804][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.815][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.816][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.817][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.819][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.820][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.834][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:46.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.853][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.854][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:46.855][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:46.856][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:46.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.864][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:46.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.870][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.871][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:46.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:46.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.884][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-31 20:44:46.885][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:46.886][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:46.895][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:46.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:46.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:46.902][biodb::testThat]
biodb.INFO [2025-08-31 20:44:46.903][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-31 20:44:46.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:46.905][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:46.908][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-31 20:44:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-31 20:44:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:46.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:46.949][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.952][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.954][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-31 20:44:46.955][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:46.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:46.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:46.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:46.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:46.981][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:46.984][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:46.986][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-31 20:44:46.987][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:46.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:46.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:46.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:46.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:46.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:46.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:46.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.035][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:47.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.056][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.057][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.058][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.060][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.061][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.063][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.065][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.066][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.069][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.071][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.073][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.075][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.076][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.091][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-31 20:44:47.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.118][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.119][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.120][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.121][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.121][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.122][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.126][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.129][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.131][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.135][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.136][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.150][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:47.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.169][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.170][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.171][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.172][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.173][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.174][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.177][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.181][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.182][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.183][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.187][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.188][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.202][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-31 20:44:47.203][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:47.204][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:47.242][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.245][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.247][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-31 20:44:47.248][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:47.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.253][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.256][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-31 20:44:47.257][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:47.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.334][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:47.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.356][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.356][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.357][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.358][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.365][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.368][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.369][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.370][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.371][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.373][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.374][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.388][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-31 20:44:47.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.409][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.410][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.411][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.412][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.417][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.422][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.423][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.430][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.435][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.436][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.449][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:47.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.471][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.472][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.481][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.482][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.484][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.485][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.487][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.488][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-31 20:44:47.502][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:47.503][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:47.511][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:47.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:47.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:47.518][biodb::testThat]
biodb.INFO [2025-08-31 20:44:47.519][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-31 20:44:47.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:47.521][biodb::testThat]
biodb.TRACE[2025-08-31 20:44:47.524][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-31 20:44:47.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-31 20:44:47.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:47.560][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.563][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.565][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-31 20:44:47.566][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:47.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-31 20:44:47.597][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.599][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.601][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-31 20:44:47.602][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:47.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:47.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.650][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:47.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.670][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.671][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.672][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.673][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.674][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.675][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.678][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.679][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.682][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.683][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.684][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.684][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.687][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.688][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.702][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-31 20:44:47.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.723][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.724][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.725][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.727][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.728][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.731][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.732][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.734][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.735][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.735][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.739][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.740][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.760][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:47.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.779][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.780][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.781][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.782][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.783][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.784][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.785][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.791][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.793][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.797][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.798][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.811][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-31 20:44:47.812][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:47.814][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:47.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:47.867][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.870][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.872][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-31 20:44:47.873][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:47.876][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:47.879][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:47.882][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-31 20:44:47.883][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:47.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:47.960][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-31 20:44:47.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:47.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:47.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:47.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:47.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:47.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:47.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.980][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.981][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:47.982][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:47.983][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:47.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.985][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.986][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.988][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.989][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.992][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.994][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:47.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:47.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:47.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:47.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:47.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-31 20:44:48.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.033][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:48.034][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:48.035][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:48.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.037][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.040][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.044][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.046][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.050][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:48.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.064][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-31 20:44:48.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.091][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-31 20:44:48.092][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-31 20:44:48.093][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-31 20:44:48.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.097][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.101][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.103][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-31 20:44:48.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.107][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.108][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-31 20:44:48.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.122][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-31 20:44:48.123][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-31 20:44:48.124][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-31 20:44:48.143][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:48.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-31 20:44:48.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:48.151][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.152][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-08-31 20:44:48.153][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.154][biodb::testThat]
biodb.DEBUG[2025-08-31 20:44:48.156][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-31 20:44:48.157][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:48.159][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:48.161][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml.
biodb.DEBUG[2025-08-31 20:44:48.162][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:48.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:48.165][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:48.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.179][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.182][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.188][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.189][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.191][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.192][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.193][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.195][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.199][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.201][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.204][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.205][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.206][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.210][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.211][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.213][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.217][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.218][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.219][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.222][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.224][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.225][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.227][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.228][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.236][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:48.278][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-31 20:44:48.279][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-31 20:44:48.286][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.288][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-31 20:44:48.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.290][biodb::testThat]
biodb.DEBUG[2025-08-31 20:44:48.298][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-31 20:44:48.300][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-31 20:44:48.301][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
fscache.INFO [2025-08-31 20:44:48.302][cch$loadContents] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:48.305][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml.
fscache.DEBUG[2025-08-31 20:44:48.308][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml.
fscache.DEBUG[2025-08-31 20:44:48.312][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml.
biodb.DEBUG[2025-08-31 20:44:48.313][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:48.315][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-31 20:44:48.316][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:48.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.329][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.332][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.337][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.338][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.340][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.342][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.344][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.346][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.349][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.354][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.355][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.357][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.359][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.360][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.363][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.364][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.368][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.371][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.373][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.377][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.378][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.380][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:48.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.436][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.437][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.439][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.444][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.445][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.447][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.449][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.453][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.456][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.464][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.470][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.471][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.473][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.478][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.479][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.481][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.483][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.487][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.490][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.492][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.496][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.497][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.499][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.505][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.508][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.513][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.515][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.516][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.518][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.525][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:48.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:48.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-31 20:44:48.576][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.579][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.585][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.586][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.589][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:48.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:48.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.593][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.594][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.595][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:48.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.601][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.602][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.604][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:48.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:48.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.609][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.610][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.612][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:48.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.617][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.618][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.620][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.621][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.625][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.626][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.628][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.629][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:48.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:48.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.634][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.635][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.636][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.642][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.645][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.650][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.653][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:48.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:48.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.659][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.660][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.662][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:48.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:48.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:48.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:48.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:48.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:48.741][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-31 20:44:48.742][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-31 20:44:48.743][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-31 20:44:48.758][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.759][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-08-31 20:44:48.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.761][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.787][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.788][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-08-31 20:44:48.789][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.790][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.798][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.799][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-08-31 20:44:48.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.801][biodb::testThat]
sched.DEBUG[2025-08-31 20:44:48.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:48.807][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:48.813][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/02ece1564def26723013d564c4071584.content.
sched.DEBUG[2025-08-31 20:44:48.814][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.TRACE[2025-08-31 20:44:48.826][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:48.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:48.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:48.831][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:48.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:48.834][ef$get] fields variable is a list.
biodb.INFO [2025-08-31 20:44:48.836][biodb::testThat]
biodb.INFO [2025-08-31 20:44:48.837][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-31 20:44:48.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:48.839][biodb::testThat]
biodb.ERROR[2025-08-31 20:44:48.854][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-31 20:44:48.873][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-31 20:44:48.885][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-31 20:44:48.887][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-31 20:44:48.888][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-31 20:44:48.889][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:48.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:48.891][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:48.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:48.899][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-31 20:44:48.912][biodb::testContext]
biodb.INFO [2025-08-31 20:44:48.913][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:48.914][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-31 20:44:48.915][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:48.916][biodb::testContext]
biodb.INFO [2025-08-31 20:44:48.918][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:48.920][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:48.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:48.924][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-31 20:44:48.925][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.929][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-31 20:44:48.930][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.933][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-31 20:44:48.934][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.938][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-31 20:44:48.939][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-31 20:44:48.940][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-31 20:44:48.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.944][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-31 20:44:48.945][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-31 20:44:48.946][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.949][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-31 20:44:48.950][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-31 20:44:48.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.954][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-31 20:44:48.955][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-31 20:44:48.956][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-31 20:44:48.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.959][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-31 20:44:48.960][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.964][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-31 20:44:48.965][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-31 20:44:48.966][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-31 20:44:48.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.969][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:48.970][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-31 20:44:48.971][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-31 20:44:48.972][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-31 20:44:48.973][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-31 20:44:48.974][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-31 20:44:48.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.977][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-31 20:44:48.979][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-31 20:44:48.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.982][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-31 20:44:48.983][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-31 20:44:48.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.986][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-31 20:44:48.988][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-31 20:44:48.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.991][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-31 20:44:48.992][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-31 20:44:48.993][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-31 20:44:48.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:48.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:48.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:48.996][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:48.997][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-31 20:44:49.001][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-31 20:44:49.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.003][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.DEBUG[2025-08-31 20:44:49.004][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-31 20:44:49.005][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-31 20:44:49.006][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-31 20:44:49.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.010][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-31 20:44:49.012][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.013][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-31 20:44:49.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:49.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.018][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.020][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:49.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:49.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.023][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-31 20:44:49.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:49.025][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:49.027][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:49.027][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:49.027][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:49.027][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:49.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:49.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:49.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.035][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:49.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:49.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.039][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.040][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-31 20:44:49.042][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.043][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:49.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:49.051][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.052][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.056][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:49.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:49.058][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.059][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-31 20:44:49.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:49.060][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.061][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.062][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:49.062][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:49.062][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:49.062][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:49.062][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:49.063][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:49.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:49.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.070][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:49.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:49.072][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.073][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.074][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-31 20:44:49.076][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.077][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-31 20:44:49.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:49.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.082][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.084][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:49.085][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:49.086][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.087][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-31 20:44:49.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:49.089][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.090][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.091][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.092][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:49.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.094][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:49.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.097][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.098][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:49.100][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:49.101][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.102][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.103][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-31 20:44:49.105][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.106][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:49.107][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.108][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:49.109][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.109][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.112][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:49.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:49.114][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.115][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-31 20:44:49.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:49.117][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.119][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:49.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:49.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.126][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.127][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:49.128][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:49.129][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.130][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:49.131][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:49.132][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.133][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[2025-08-31 20:44:49.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.160][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[2025-08-31 20:44:49.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.177][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[2025-08-31 20:44:49.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.211][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-31 20:44:49.213][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-31 20:44:49.214][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-31 20:44:49.217][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-31 20:44:49.218][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:49.219][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-31 20:44:49.221][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:49.222][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:49.223][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-31 20:44:49.225][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-31 20:44:49.226][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:49.227][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-31 20:44:49.229][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:49.230][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:49.231][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-31 20:44:49.233][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-31 20:44:49.234][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-31 20:44:49.236][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-31 20:44:49.237][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:49.238][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-31 20:44:49.240][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-31 20:44:49.241][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-31 20:44:49.243][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-31 20:44:49.244][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-31 20:44:49.245][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-31 20:44:49.247][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-31 20:44:49.248][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-31 20:44:49.250][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-31 20:44:49.251][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-31 20:44:49.252][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-31 20:44:49.254][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-31 20:44:49.255][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-31 20:44:49.256][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-31 20:44:49.258][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-31 20:44:49.259][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-31 20:44:49.260][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-31 20:44:49.262][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-31 20:44:49.263][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-31 20:44:49.265][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-31 20:44:49.266][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-31 20:44:49.267][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-31 20:44:49.269][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-31 20:44:49.270][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-31 20:44:49.272][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-31 20:44:49.273][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-31 20:44:49.274][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-31 20:44:49.276][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-31 20:44:49.277][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-31 20:44:49.279][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-31 20:44:49.280][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-31 20:44:49.281][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-31 20:44:49.283][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-31 20:44:49.284][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-31 20:44:49.286][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-31 20:44:49.287][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-31 20:44:49.288][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-31 20:44:49.290][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-31 20:44:49.291][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-31 20:44:49.292][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-31 20:44:49.294][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-31 20:44:49.295][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-31 20:44:49.297][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-31 20:44:49.298][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-31 20:44:49.300][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-31 20:44:49.301][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-31 20:44:49.302][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-31 20:44:49.304][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:49.305][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:49.306][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-31 20:44:49.308][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-31 20:44:49.309][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-31 20:44:49.311][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-31 20:44:49.312][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-31 20:44:49.314][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-31 20:44:49.315][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-31 20:44:49.316][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-31 20:44:49.318][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-31 20:44:49.319][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-31 20:44:49.320][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-31 20:44:49.322][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-31 20:44:49.323][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-31 20:44:49.324][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-31 20:44:49.326][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-31 20:44:49.327][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-31 20:44:49.329][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:49.330][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:49.331][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.332][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.620][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.DEBUG[2025-08-31 20:44:49.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.628][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:49.637][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-31 20:44:49.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.640][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:49.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.645][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.646][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-31 20:44:49.647][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-31 20:44:49.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:49.649][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.650][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-31 20:44:49.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-31 20:44:49.652][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-31 20:44:49.653][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:49.654][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:49.654][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:49.654][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:49.655][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-31 20:44:49.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:49.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:49.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:49.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:49.662][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-31 20:44:49.662][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-31 20:44:49.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:49.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:49.664][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:49.665][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-31 20:44:49.665][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-31 20:44:49.667][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:49.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:49.670][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-31 20:44:49.671][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:49.673][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:49.674][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:49.678][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-31 20:44:49.681][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-31 20:44:49.683][biodb::testThat]
biodb.INFO [2025-08-31 20:44:49.684][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-08-31 20:44:49.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:49.686][biodb::testThat]
sched.DEBUG[2025-08-31 20:44:49.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-31 20:44:49.692][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.698][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-31 20:44:49.699][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:49.703][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".
fscache.INFO [2025-08-31 20:44:49.726][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.729][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-31 20:44:49.731][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.745][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".
fscache.INFO [2025-08-31 20:44:49.748][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.750][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-31 20:44:49.752][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.764][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.DEBUG[2025-08-31 20:44:49.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.796][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".
sched.DEBUG[2025-08-31 20:44:49.801][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".
fscache.INFO [2025-08-31 20:44:49.805][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.807][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-31 20:44:49.808][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.822][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".
fscache.INFO [2025-08-31 20:44:49.825][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.832][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-31 20:44:49.833][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.844][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[2025-08-31 20:44:49.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.858][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".
fscache.INFO [2025-08-31 20:44:49.860][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.862][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-31 20:44:49.863][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.875][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".
fscache.INFO [2025-08-31 20:44:49.878][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.880][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-31 20:44:49.881][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.893][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".
fscache.INFO [2025-08-31 20:44:49.895][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.898][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/d853ab8a48594978d76c30b86726648a.content.
sched.DEBUG[2025-08-31 20:44:49.898][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-31 20:44:49.916][biodb::testThat]
biodb.INFO [2025-08-31 20:44:49.917][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-08-31 20:44:49.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:49.919][biodb::testThat]
sched.DEBUG[2025-08-31 20:44:49.922][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".
fscache.INFO [2025-08-31 20:44:49.925][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.927][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/aa56e28005d49da17591454624aabcd2.content.
sched.DEBUG[2025-08-31 20:44:49.928][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-31 20:44:49.944][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".
fscache.INFO [2025-08-31 20:44:49.947][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:49.949][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/c62078a064e3122e21e26c3428179396.content.
sched.DEBUG[2025-08-31 20:44:49.950][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:49.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:49.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-31 20:44:49.965][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-31 20:44:49.966][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-31 20:44:49.967][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-31 20:44:49.968][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:49.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:49.970][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:49.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:49.971][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.972][FUN] Functions in observer BiodbConfig: [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 [2025-08-31 20:44:49.976][biodb::testContext]
biodb.INFO [2025-08-31 20:44:49.977][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:49.978][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-31 20:44:49.978][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:49.979][biodb::testContext]
biodb.INFO [2025-08-31 20:44:49.981][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:49.983][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:49.987][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:49.988][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-31 20:44:49.989][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-31 20:44:49.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.992][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-31 20:44:49.993][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-31 20:44:49.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:49.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:49.997][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-31 20:44:49.997][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-31 20:44:49.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:49.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.001][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-31 20:44:50.002][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-31 20:44:50.003][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.005][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.DEBUG[2025-08-31 20:44:50.006][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-31 20:44:50.007][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-31 20:44:50.008][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.012][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-31 20:44:50.013][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.016][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-31 20:44:50.017][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-31 20:44:50.018][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-31 20:44:50.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.021][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-31 20:44:50.022][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.026][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-31 20:44:50.027][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-31 20:44:50.028][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.031][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:50.032][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-31 20:44:50.033][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-31 20:44:50.034][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-31 20:44:50.035][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-31 20:44:50.036][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-31 20:44:50.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.038][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[2025-08-31 20:44:50.039][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-31 20:44:50.040][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-31 20:44:50.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.044][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-31 20:44:50.045][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-31 20:44:50.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.047][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[2025-08-31 20:44:50.048][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-31 20:44:50.049][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.052][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-31 20:44:50.053][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-31 20:44:50.054][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-31 20:44:50.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.057][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[2025-08-31 20:44:50.058][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:50.059][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-31 20:44:50.062][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-31 20:44:50.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.066][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-31 20:44:50.067][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-31 20:44:50.068][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-31 20:44:50.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.071][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-31 20:44:50.073][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.074][self$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[2025-08-31 20:44:50.075][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.076][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.077][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.078][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.079][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.080][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.081][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:50.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.083][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.084][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-31 20:44:50.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.085][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.086][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.087][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:50.087][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:50.087][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:50.087][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:50.087][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:50.088][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.091][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.094][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.095][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.096][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.097][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.097][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.098][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.100][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-31 20:44:50.101][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.102][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:50.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.108][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.109][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:50.110][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.112][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-31 20:44:50.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.114][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.115][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.116][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:50.116][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:50.116][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:50.116][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:50.116][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:50.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.127][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.130][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.131][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.132][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-31 20:44:50.134][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.135][self$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[2025-08-31 20:44:50.136][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.137][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.139][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.140][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.141][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:50.142][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.143][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.144][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-31 20:44:50.145][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.146][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.148][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.155][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.156][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.157][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.158][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.159][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-31 20:44:50.161][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.162][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:50.163][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.164][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.165][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.166][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.167][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.168][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.169][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:50.170][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.171][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.172][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-31 20:44:50.172][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.173][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.174][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.175][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.176][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.181][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.182][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.185][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.186][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.187][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:50.188][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.189][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.DEBUG[2025-08-31 20:44:50.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.205][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[2025-08-31 20:44:50.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.234][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[2025-08-31 20:44:50.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.243][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[2025-08-31 20:44:50.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.255][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[2025-08-31 20:44:50.256][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-31 20:44:50.258][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-31 20:44:50.259][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-31 20:44:50.261][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-31 20:44:50.262][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:50.263][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-31 20:44:50.265][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:50.266][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:50.267][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-31 20:44:50.268][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-31 20:44:50.270][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:50.271][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-31 20:44:50.272][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:50.274][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:50.275][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-31 20:44:50.276][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-31 20:44:50.278][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-31 20:44:50.279][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-31 20:44:50.280][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:50.282][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-31 20:44:50.283][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-31 20:44:50.284][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-31 20:44:50.286][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-31 20:44:50.287][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-31 20:44:50.289][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-31 20:44:50.290][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-31 20:44:50.291][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-31 20:44:50.293][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-31 20:44:50.294][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-31 20:44:50.295][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-31 20:44:50.297][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-31 20:44:50.298][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-31 20:44:50.299][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-31 20:44:50.301][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-31 20:44:50.302][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-31 20:44:50.303][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-31 20:44:50.305][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-31 20:44:50.306][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-31 20:44:50.307][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-31 20:44:50.309][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-31 20:44:50.310][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-31 20:44:50.311][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-31 20:44:50.313][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-31 20:44:50.314][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-31 20:44:50.315][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-31 20:44:50.317][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-31 20:44:50.318][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-31 20:44:50.319][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-31 20:44:50.321][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-31 20:44:50.322][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-31 20:44:50.323][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-31 20:44:50.325][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-31 20:44:50.326][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-31 20:44:50.327][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-31 20:44:50.329][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-31 20:44:50.330][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-31 20:44:50.331][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-31 20:44:50.333][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-31 20:44:50.334][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-31 20:44:50.336][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-31 20:44:50.337][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-31 20:44:50.338][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-31 20:44:50.340][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-31 20:44:50.341][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-31 20:44:50.342][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-31 20:44:50.344][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-31 20:44:50.345][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:50.346][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:50.348][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-31 20:44:50.349][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-31 20:44:50.350][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-31 20:44:50.352][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-31 20:44:50.353][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-31 20:44:50.354][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-31 20:44:50.356][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-31 20:44:50.357][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-31 20:44:50.358][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-31 20:44:50.360][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-31 20:44:50.361][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-31 20:44:50.363][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-31 20:44:50.364][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-31 20:44:50.365][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-31 20:44:50.367][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-31 20:44:50.368][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-31 20:44:50.370][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:50.371][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:50.372][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.374][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.393][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[2025-08-31 20:44:50.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.399][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[2025-08-31 20:44:50.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.429][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[2025-08-31 20:44:50.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.434][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[2025-08-31 20:44:50.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.446][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[2025-08-31 20:44:50.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.452][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[2025-08-31 20:44:50.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.458][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[2025-08-31 20:44:50.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.464][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[2025-08-31 20:44:50.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.470][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[2025-08-31 20:44:50.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.476][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[2025-08-31 20:44:50.477][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:50.479][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-31 20:44:50.480][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.481][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.484][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.485][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.486][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.487][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-31 20:44:50.488][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-31 20:44:50.489][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.490][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.491][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-31 20:44:50.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-31 20:44:50.493][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-31 20:44:50.494][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:50.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:50.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:50.496][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-31 20:44:50.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.498][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.501][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.502][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-31 20:44:50.502][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-31 20:44:50.503][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.505][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.506][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-31 20:44:50.506][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-31 20:44:50.507][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:50.509][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:50.510][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-31 20:44:50.512][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:50.514][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:50.515][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:50.519][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-31 20:44:50.522][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-31 20:44:50.524][biodb::testThat]
biodb.INFO [2025-08-31 20:44:50.525][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-31 20:44:50.526][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:50.527][biodb::testThat]
sched.DEBUG[2025-08-31 20:44:50.529][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-31 20:44:50.531][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:50.537][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-31 20:44:50.538][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:50.542][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
fscache.INFO [2025-08-31 20:44:50.544][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:50.546][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content.
sched.DEBUG[2025-08-31 20:44:50.547][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.INFO [2025-08-31 20:44:50.555][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-31 20:44:50.556][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-31 20:44:50.557][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-31 20:44:50.558][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.560][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.562][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-31 20:44:50.567][biodb::testContext]
biodb.INFO [2025-08-31 20:44:50.568][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:50.569][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-31 20:44:50.570][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-31 20:44:50.571][biodb::testContext]
biodb.INFO [2025-08-31 20:44:50.573][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:50.575][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:50.579][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:50.580][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-31 20:44:50.581][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.585][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-31 20:44:50.586][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.590][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-31 20:44:50.591][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.595][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-31 20:44:50.596][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-31 20:44:50.597][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.601][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-31 20:44:50.602][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-31 20:44:50.603][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.606][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-31 20:44:50.607][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.611][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-31 20:44:50.612][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-31 20:44:50.613][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-31 20:44:50.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.617][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-31 20:44:50.618][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.621][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-31 20:44:50.622][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-31 20:44:50.624][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-31 20:44:50.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.627][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:50.628][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-31 20:44:50.629][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-31 20:44:50.630][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-31 20:44:50.631][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-31 20:44:50.632][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-31 20:44:50.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.636][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-31 20:44:50.637][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-31 20:44:50.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.640][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[2025-08-31 20:44:50.641][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-31 20:44:50.643][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-31 20:44:50.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.647][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-31 20:44:50.648][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-31 20:44:50.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.651][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-31 20:44:50.652][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-31 20:44:50.653][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-31 20:44:50.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.657][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-31 20:44:50.658][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-31 20:44:50.662][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-31 20:44:50.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.664][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[2025-08-31 20:44:50.665][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-31 20:44:50.672][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-31 20:44:50.673][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-31 20:44:50.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.677][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-31 20:44:50.678][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.679][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-31 20:44:50.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.682][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.683][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.684][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.685][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.686][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:50.687][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.688][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.689][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-31 20:44:50.690][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.691][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.692][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.693][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:50.693][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:50.693][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:50.693][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:50.693][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:50.694][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.695][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.696][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.699][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.700][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.703][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.705][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-31 20:44:50.706][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.707][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:50.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.712][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.714][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:50.715][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.716][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.717][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-31 20:44:50.718][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.719][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.720][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.721][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:50.721][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:50.721][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:50.721][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-31 20:44:50.721][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-31 20:44:50.722][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.725][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.728][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.729][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.730][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.731][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.732][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.733][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-31 20:44:50.735][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-31 20:44:50.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.742][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.743][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-31 20:44:50.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.745][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.745][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-31 20:44:50.746][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.747][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.748][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.749][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.756][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.760][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.761][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-31 20:44:50.763][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.764][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-31 20:44:50.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:50.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.769][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.770][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.771][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-31 20:44:50.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:50.773][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.774][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-31 20:44:50.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:50.776][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:50.778][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.779][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-31 20:44:50.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.781][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:50.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:50.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:50.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:50.785][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:50.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:50.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:50.789][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-31 20:44:50.790][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:50.791][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.814][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.DEBUG[2025-08-31 20:44:50.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.819][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[2025-08-31 20:44:50.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.832][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[2025-08-31 20:44:50.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.836][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[2025-08-31 20:44:50.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.849][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[2025-08-31 20:44:50.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.853][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[2025-08-31 20:44:50.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.863][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-31 20:44:50.865][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-31 20:44:50.866][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-31 20:44:50.867][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-31 20:44:50.869][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:50.870][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-31 20:44:50.872][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:50.873][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:50.874][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-31 20:44:50.876][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-31 20:44:50.877][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:50.879][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-31 20:44:50.880][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-31 20:44:50.882][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-31 20:44:50.883][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-31 20:44:50.884][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-31 20:44:50.886][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-31 20:44:50.887][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-31 20:44:50.889][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:50.890][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-31 20:44:50.891][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-31 20:44:50.893][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-31 20:44:50.894][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-31 20:44:50.896][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-31 20:44:50.897][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-31 20:44:50.898][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-31 20:44:50.900][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-31 20:44:50.901][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-31 20:44:50.903][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-31 20:44:50.904][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-31 20:44:50.905][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-31 20:44:50.907][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-31 20:44:50.908][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-31 20:44:50.909][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-31 20:44:50.911][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-31 20:44:50.912][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-31 20:44:50.913][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-31 20:44:50.915][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-31 20:44:50.916][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-31 20:44:50.917][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-31 20:44:50.919][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-31 20:44:50.920][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-31 20:44:50.921][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-31 20:44:50.923][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-31 20:44:50.924][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-31 20:44:50.925][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-31 20:44:50.927][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-31 20:44:50.928][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-31 20:44:50.930][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-31 20:44:50.931][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-31 20:44:50.932][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-31 20:44:50.938][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-31 20:44:50.940][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-31 20:44:50.941][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-31 20:44:50.942][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-31 20:44:50.944][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-31 20:44:50.945][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-31 20:44:50.946][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-31 20:44:50.948][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-31 20:44:50.949][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-31 20:44:50.950][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-31 20:44:50.952][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-31 20:44:50.953][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-31 20:44:50.954][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-31 20:44:50.956][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-31 20:44:50.957][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-31 20:44:50.958][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:50.960][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:50.961][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-31 20:44:50.962][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-31 20:44:50.964][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-31 20:44:50.965][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-31 20:44:50.966][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-31 20:44:50.968][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-31 20:44:50.969][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-31 20:44:50.970][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-31 20:44:50.972][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-31 20:44:50.973][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-31 20:44:50.974][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-31 20:44:50.975][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-31 20:44:50.977][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-31 20:44:50.978][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-31 20:44:50.979][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-31 20:44:50.981][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-31 20:44:50.982][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-31 20:44:50.983][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-31 20:44:50.984][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.986][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:50.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:50.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:50.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:50.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:50.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:50.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.040][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[2025-08-31 20:44:51.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.046][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[2025-08-31 20:44:51.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.064][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[2025-08-31 20:44:51.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-31 20:44:51.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-31 20:44:51.083][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-31 20:44:51.084][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-31 20:44:51.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:51.087][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-31 20:44:51.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:51.089][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-31 20:44:51.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:51.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-31 20:44:51.092][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:51.093][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-31 20:44:51.094][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-31 20:44:51.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-31 20:44:51.096][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:51.097][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-31 20:44:51.098][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-31 20:44:51.099][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-31 20:44:51.100][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-31 20:44:51.101][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-31 20:44:51.101][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-31 20:44:51.101][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-31 20:44:51.102][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-31 20:44:51.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:51.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:51.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-31 20:44:51.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-31 20:44:51.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-31 20:44:51.107][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-31 20:44:51.108][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-31 20:44:51.108][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-31 20:44:51.109][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-31 20:44:51.110][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-31 20:44:51.111][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-31 20:44:51.112][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-31 20:44:51.112][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-31 20:44:51.113][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-31 20:44:51.115][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-31 20:44:51.117][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-31 20:44:51.118][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-31 20:44:51.120][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-31 20:44:51.121][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-31 20:44:51.125][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-31 20:44:51.128][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-31 20:44:51.130][biodb::testThat]
biodb.INFO [2025-08-31 20:44:51.131][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-31 20:44:51.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-31 20:44:51.133][biodb::testThat]
sched.DEBUG[2025-08-31 20:44:51.135][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-31 20:44:51.137][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:51.143][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-31 20:44:51.144][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-31 20:44:51.148][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".
fscache.INFO [2025-08-31 20:44:51.151][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-31 20:44:51.153][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content.
sched.DEBUG[2025-08-31 20:44:51.154][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-31 20:44:51.159][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-31 20:44:51.162][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-31 20:44:51.164][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-31 20:44:51.173][FUN] Found encoding UTF-8 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml.
biodb.DEBUG[2025-08-31 20:44:51.175][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-31 20:44:51.177][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-31 20:44:51.178][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-31 20:44:51.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-31 20:44:51.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.190][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.TRACE[2025-08-31 20:44:51.194][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.197][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.202][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:51.203][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:51.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.205][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.207][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-31 20:44:51.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-31 20:44:51.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.211][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:51.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:51.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.214][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-31 20:44:51.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-31 20:44:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.229][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-31 20:44:51.230][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-31 20:44:51.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.233][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.235][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-31 20:44:51.256][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-31 20:44:51.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.258][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:51.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:51.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.264][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.266][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:51.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-31 20:44:51.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.270][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:51.271][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:51.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.273][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.275][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-31 20:44:51.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-31 20:44:51.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.279][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:51.280][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:51.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.282][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:51.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-31 20:44:51.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.288][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:51.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:51.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-31 20:44:51.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-31 20:44:51.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.298][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:51.299][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:51.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.301][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-31 20:44:51.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-31 20:44:51.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.307][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:51.308][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:51.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.310][ef$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-31 20:44:51.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-31 20:44:51.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-31 20:44:51.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-31 20:44:51.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-31 20:44:51.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-31 20:44:51.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-31 20:44:51.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-31 20:44:51.358][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-31 20:44:51.362][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-31 20:44:51.363][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-31 20:44:51.364][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-31 20:44:51.365][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-31 20:44:51.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-31 20:44:51.367][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-31 20:44:51.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-31 20:44:51.369][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-31 20:44:51.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 357 ]
> 
> proc.time()
   user  system elapsed 
 15.294   0.474  17.620

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.7200.0690.797
ChebiEntry0.1920.0190.209